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NAMD User`s Guide

1. e FMALevels lt number of levels to use in multipole expansion gt Acceptable Values positive integer Default Value 5 Description Number of levels to use for the multipole expansion This parameter is only used if FMA is set to on A value of 4 should be sufficient for systems with less than 10 000 atoms A value of 5 or greater should be used for larger systems e FMAMp lt number of multipole terms to use for FMA gt Acceptable Values positive integer Default Value 8 Description Number of terms to use in the multipole expansion This parameter is only used if FMA is set to on If the FMAFFT is set to on then this value must be a multiple of 4 The default value of 8 should be suitable for most applications e FMAFFT lt use DPMTA FFT enhancement gt Acceptable Values on or off Default Value on Description Specifies whether or not the DPMTA code should use the FFT enhancement feature This parameter is only used if FMA is set to on If FMAFFT is set to on the value of FMAMp must be set to a multiple of 4 This feature offers substantial benefits only for values of FMAMp of 8 or greater This feature will substantially increase the amount of memory used by DPMTA e FMAtheta lt DPMTA theta parameter radians gt Acceptable Values decimal Default Value 0 715 48 Description This parameter specifies the value of the theta parameter used in the DPMTA calculation The default value is based on recommendations by the d
2. langevinTemp lt temperature for Langevin calculations K gt Acceptable Values positive decimal Description Temperature to which atoms affected by Langevin dynamics will be adjusted This temperature will be roughly maintained across the affected atoms through the addition of friction and random forces langevinDamping lt damping coefficient for Langevin dynamics 1 ps gt Acceptable Values positive decimal Default Value per atom values from PDB file Description Langevin coupling coefficient to be applied to all atoms unless langevinHydrogen is off in which case only non hydrogen atoms are affected If not given a PDB file is used to obtain coefficients for each atom see langevinFile and langevinCol below langevinHydrogen lt Apply Langevin dynamics to hydrogen atoms gt Acceptable Values on or off Default Value on Description If langevinDamping is set then setting langevinHydrogen to off will turn off Langevin dynamics for hydrogen atoms This parameter has no effect if Langevin coupling coefficients are read from a PDB file langevinFile lt PDB file containing Langevin parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the Langevin coupling coefficients for each atom If this parameter is not specified then the PDB file specified by coordinates is used langevinCol lt column of PDB from which to read coefficients gt Acceptable Values X
3. segname resnum to segname resnum Example group insulin 10 to insulin 12 One or more atomnames in a list of residues group atomname segname resnum segname resnum group atomname atomname segname resnum segname resnum Examples group ca insulin 10 insulin 12 insulin 14 group ca cb cg insulin 10 insulin 12 insulin 14 group ca cb insulin 10 insulin 12 cg insulin 11 insulin 12 Note Within a group atomname is in effect until a new atomname is used or the keyword all is used atomname will not carry over from group to group This note applies to the paragraph below One or more atomnames in a range of residues group atomname segname resnum to segname resnum group atomname atomname segname resnum to segname resnum Examples group ca insulin 10 to insulin 14 group ca cb cg insulin 10 to insulin 12 group ca cb insulin 10 to insulin 12 all insulin 13 6 7 5 Options for Potential of Mean Force Calculation The pmf and mcti blocks below are used to simultaneously control all forcing restraints specified in urestraint above These blocks are performed consecutively in the order they appear in the 78 config file The pmf block is used to either a smoothly vary A from 0 1 or 1 0 or b set lambda The mcti block is used to vary A from 0 1 or 1 0 in
4. 57 tCoupleCol parameter 57 tCoupleFile parameter 57 tCoupleTemp parameter 57 TEMPAVG 22 temperature parameter 46 timestep parameter 43 topology psfgen command 34 TOTAL2 energy 22 TOTALS energy 22 units used for output 22 useConstantArea parameter 63 useConstantRatio parameter 63 useDPME parameter 50 useF lexibleCell parameter 63 useGroupPressure parameter 63 useSettle parameter 47 velDCDfile parameter 21 velDCDfreq parameter 21 velocities parameter 19 velocityQuenching parameter 55 wrapAll parameter 62 wrapNearest parameter 62 wrap Water parameter 62 writepdb psfgen command 37 writepsf psfgen command 37 XSTfile parameter 61 XSTfreq parameter 61 113
5. 6 and X PLOR 7 This force field includes local interaction terms consisting of bonded interactions between 2 3 and 4 atoms and pairwise interactions including electrostatic and van der Waals forces This commonality allows simulations to migrate between these three programs e Efficient Full Electrostatics Algorithms NAMD incorporates the Particle Mesh Ewald PME algorithm which takes the full elec trostatic interactions into account This algorithm reduces the computational complexity of electrostatic force evaluation from O N to O N log N e Multiple Time Stepping The velocity Verlet integration method 1 is used to advance the positions and velocities of the atoms in time To further reduce the cost of the evaluation of long range electrostatic forces a multiple time step scheme is employed The local interactions bonded van der Waals and electrostatic interactions within a specified distance are calculated at each time step The longer range interactions electrostatic interactions beyond the specified distance are only computed less often This amortizes the cost of computing the electrostatic forces over several timesteps A smooth splitting function is used to separate a quickly varying short range portion of the electrostatic interaction from a more slowly varying long range component It is also possible to employ an intermediate timestep for the short range non bonded interactions performing only bonded interactions every
6. 7 20 2D k V ps yo yp i 2D 20 j 0 0 F V pa 0 0 F zo za j ya yc k V ps 24 20 1 0 0 7 2c za Jk Vips yo ya i ea 2c 7 0 0 F Gradient for forcing position restraint E KAIR Frefl Tref ATI 1 A T 2 2 2 1 2 dE dd Kpx ai tref Yi Yres zi Zreg x 1 2 G Tref y Yref zi R 2re 2 i Tres o 1 2 Yi Yres Yo Ya 2 zi 2ref 20 21 i Tref o 21 Yi Yres Yo Y1 zi 2ref 20 21 1 2 dE dd Ky x a Gradient for forcing stretch restraint E K5 2 di dref dref Ad 1 A do dE dx Ky x d dref x do d Gradient for forcing bend restraint E Ky 2 0 Ores Oref M0 1 A Oo dE dx Ky x 6 Oreg x 00 01 83 Gradient for forcing dihedral restraint E Eo 2 1 COS Xi z Xref Xref AX1 1 A xo dE dA E0 2 x sin xi Xref x x0 X1 6 8 Alchemical Free Energy Perturbation Calculations This feature has been contributed to NAMD by the following authors Surjit B Dixit and Christophe Chipot Equipe de dynamique des assemblages membranaires Institut nanc ien de chimie mol culaire UMR CNRS UHP 7565 Universit Henri Poincar BP 239 54506 Vandeeuvre l s Nancy cedex France 6 8 1 Introduction and theoretical background A method to perform alchemical free energy
7. Description The final temperature for reassignment when reassignIncr is set reassignTemp will be held at this value once it has been reached This parameter is valid only if reassignIncr has been set 6 4 Boundary Conditions 6 4 1 Spherical harmonic boundary conditions NAMD provides spherical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions e sphericalBC lt use spherical boundary conditions gt Acceptable Values on or off Default Value off 58 Description Specifies whether or not spherical boundary conditions are to be applied to the system If set to on then sphericalBCCenter sphericalBCr1 and sphericalBCk1 must be defined and sphericalBCexp1 sphericalBCr2 sphericalBCk2 and sphericalBCexp2 can optionally be defined e sphericalBCCenter lt center of sphere A gt Acceptable Values position Description Location around which sphere is centered e sphericalBCri lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect This distance is a radius from the center e sphericalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal Description Force constant for the first harmonic potential A positive value will push atoms
8. The atoms representative of state a do not interact with those of state b throughout the entire molecular dynamics simulation Such a setup in which atoms pertaining to both the initial and the final states of the system are present in the molecular topology file i e the psf file is referred to as dual topology paradigm 2 15 The hybrid Hamiltonian of the 84 system which is a function of the coupling parameter A that smoothly connects state a to state b is evaluated as H A Ho AHa 1 AV 5 where Ha is the Hamiltonian for the group of atoms representative of the initial state a and H characterizes the final state b Ho is the Hamiltonian for those atoms that do not undergo any transformation during the MD simulation For instance in a transformation involving the mutation of an alanine side chain into that of glycine using the FEP methodology the topology of both the methyl group of alanine and the hydrogen borne by the Ca in glycine co exist throughout the simulation see Figure 5 JE antl Not N Figure 5 Dual topology description for an alchemical simulation Case example of the mutation of alanine into glycine The lighter color denotes the non interacting alternate state The energy and forces are defined as a function of A in such a fashion that the interaction of the methyl group of alanine with the rest of the protein is effective at the beginning of the simulation i e 0
9. amp ewald PME on Use PME for electrostatic calculation Orthogonal periodic box size a 62 23 cellBasisVector1 62 23 0 O b 62 23 cellBasisVector2 O 62 23 0 c 62 23 cellBasisVector3 O O 62 23 nfft1 64 PMEGridSizeX 64 nfft2 64 PMEGridSizeY 64 nfft3 64 PMEGridSizeZ 64 ischrgd 1 NAMD doesn t force neutralization of charge amp end amber on Specify this is AMBER force field parmfile FILENAME Input PARM file ambercoor FILENAME Input coordinate file outputname PREFIX Prefix of output files exclude scaled1 4 1 4scaling 0 833333 1 1 2 default is 1 0 3 4 GROMACS force field paramets NAMD has the ability to load GROMACS ASCII topology top and coordinate gro files which allows you to run most GROMACS simulations in NAMD All simulation output will still be in the traditional NAMD formats e gromacs lt use GROMACS format force field gt Acceptable Values on or off Default Value off Description If gromacs is set to on then grotopfile must be defined and structure and parameters should not be defined e grotopfile lt GROMACS format topology parameter file gt Acceptable Values UNIX filename 25 Description This file contains complete topology and parameter information of the system e grocoorfile lt GROMACS format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates can also be used for PDB format coordinate
10. lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector2 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cellBasisVector3 lt basis vector for periodic boundaries A gt Acceptable Values vector Default Value 000 Description Specifies a basis vector for periodic boundary conditions e cell0rigin lt center of periodic cell A gt Acceptable Values position Default Value 000 Description When position rescaling is used to control pressure this location will remain constant Also used as the center of the cell for wrapped output coordinates e extendedSystem lt XSC file to read cell parameters from gt Acceptable Values file name Description In addition to coor and vel output files NAMD generates a xsc eXtended System Configuration file which contains the periodic cell parameters and extended system variables such as the strain rate in constant pressure simulations Periodic cell parameters will be read from this file if this option is present ignoring the above parameters e XSTfile lt XST file to write cell trajectory to gt Acceptable Values file name Description _NAMD can also generate a xst eXtended System Trajectory file which contains a record of the peri
11. no Description If no NAMD will proceed with calculations whether a connection is present or not If yes NAMD will pause at startup until a connection is made and pause when the connection is lost e IMDignore lt ignore interactive steering forces gt Acceptable Values yes or no Default Value no Description If yes NAMD will ignore any steering forces generated by VMD to allow a simulation to be monitored without the possibility of perturbing it 6 6 7 Tcl interface NAMD provides a limited Tcl scripting interface designed for applying forces and performing on the fly analysis This interface is efficient if only a few coordinates either of individual atoms or centers of mass of groups of atoms are needed In addition information must be requested one timestep in advance The following configuration parameters are used to enable the Tcl interface e tclForces lt is Tcl interface active gt Acceptable Values on or off Default Value off Description Specifies whether or not Tcl interface is active If it is set to off then no Tcl code is executed If it is set to on then Tcl code specified in tclForcesScript parameters is executed e tclForcesScript lt input for Tcl interface gt Acceptable Values file or script Description Must contain either the name of a Tcl script file or the script itself between and may include multiple lines This parameter may occur multiple times and scripts will be executed in order
12. or creating disulphide bonds between a pair of residues Arguments lt patch residue name gt Name of patch residue from topology definition file lt segid resid gt List of segment and residue pairs to which patch should be applied Context After one or more segments have been built 35 regenerate angles dihedrals Purpose Remove all angles and or dihedrals and completely regenerate them using the segment automatic generation algorithms This is only needed if patches were applied that do not correct angles and bonds Segment and file defaults are ignored and angles dihedrals for the entire molecule are regenerated from scratch Arguments angles Enable generation of angles from bonds dihedrals Enable generation of dihedrals from angles Context After one or more segments have been built multiply lt factor gt lt segid resid atomnamej gt Purpose Create multiple images of a set of atoms for use in locally enhanced sampling The beta column of the output pdb file is set to 1 lt factor gt for each image Multiple copies of bonds angles etc are created Atom residue or segment names are not altered images are distinguished only by beta value This is not a normal molecular structure and may confuse other tools Arguments lt factor gt lt segid resid atomname gt segment residue or atom to be multiplied If resid is omitted the entire segment is multiplied if atomname is omitted the entire residu
13. reassignFreq parameter 58 reassignHold parameter 58 reassignIncr parameter 58 reassignTemp parameter 58 regenerate psfgen command 36 reinitvels command 16 rescaleFreq parameter 57 rescaleTemp parameter 58 rescalevels command 16 resetpsf psfgen command 36 residue psfgen command 35 restartfreq parameter 21 restartname parameter 20 restartsave parameter 21 rigidBonds parameter 47 rigidDieOnError parameter 47 rigidIterations parameter 47 rigidTolerance parameter 47 rotConsAxis parameter 69 rotConsPivot parameter 69 rotConstraints parameter 68 rotConsVel parameter 69 run command 15 scnb parameter 23 seed parameter 47 segment psfgen command 34 selectConstraints parameter 54 selectConstrX parameter 54 selectConstrY parameter 54 selectConstrZ parameter 54 SMD parameter 70 SMDDir parameter 70 SMDFile parameter 70 112 SMDKk parameter 70 SMDOutputFreq parameter 70 SMDVel parameter 70 source command 15 sphericalBC parameter 58 sphericalBCCenter parameter 59 sphericalBCexp1 parameter 59 sphericalBCexp2 parameter 59 sphericalBCk1 parameter 59 sphericalBCk2 parameter 59 sphericalBCr1 parameter 59 sphericalBCr2 parameter 59 splitPatch parameter 44 stepspercycle parameter 43 StrainRate parameter 66 structure parameter 19 Surface TensionTarget parameter 65 switchdist parameter 44 switching parameter 44 tclForces parameter 71 tclForcesScript parameter 71 tCouple parameter
14. while the glycine Ca hydrogen does not interact with the rest of the protein and vice versa at the end of the simulation 7 e A 1 For intermediate values of A both the alanine and the glycine side chains participate in the non bonded interactions with the rest of the protein scaled on the basis of the current value of A It should be emphasized that these side chains however do not interact with each other It is therefore necessary to exclude explicitly in the setup those atoms that are created from those that will be annihilated in the course of the FEP calculation see A tutorial to set up alchemical free energy perturbation calculations in NAMD available from the NAMD website It is also worth noting that the free energy calculation does not alter intramolecular potentials i e bond stretch valence angle deformation torsions etc during the simulation In calculations targetted at the estimation of free energy differences between two states characterized by distinct environments e g a ligand bound to a protein in the first simulation and solvated in water in the second as is the case for most free energy calculations that make use of a thermodynamic cycle perturbation of intramolecular terms e g chemical bonds can be safely avoided 5 6 8 2 Implementation of free energy perturbation in NAMD The procedure implemented in NAMD is particularly adapted for performing free energy calcula tions that split the reaction pa
15. x1 X2 lt x Axa And E G 2 1 cos x x2 x2 4x lt x x Ax 27 E G G Eo 1 cos Ax Bounds may be used in pairs to set a lower and upper bound Torsional bounds always are defined in pairs 6 7 2 Free Energy Calculations Conformational forcing Potential of mean force In conformational forcing calculations structural parameters such as atomic positions inter atomic distances and dihedral angles are forced to change by application of changing restraint potentials For example the distance between two atoms can be restrained by a potential to a mean distance that is varied during the calculation The free energy change or potential of mean force pmf for the process can be estimated during the simulation The potential is made to depend on a coupling parameter A whose value changes during the simulation In potential of mean force calculations the reference value of the restraint potential depends on A Alternately the force constant for the restraint potential may change in proportion to the coupling parameter Such a calculation gives the value of a restraint free energy i e the free energy change of the system due to imposition of the restraint potential Methods for computing the free energy With conformational forcing or with molecular transformation calculations one obtains a free energy difference for a process that is forced on the system by changing the potential energy function that deter
16. 2a yo ya F 20 za b V a zc xB yc yB zc zB E a Gradient for dihedral angle restraint E Eo 2 1 COS Xi Xref Atoms at positions A B C D Xi cos u cos ea BO lt BA AND x sey a CDxCB x BCxBA TB ae 7 OBOB BCxBA CE V E Fo 2 sin xi Xref V xi Voa 725 Vu CDxCB yp yc ze zo zp 2c ye yo ce zp 2c tB c p tc 2B 2c j up to YB yc yo yo eB 20 k pit poj p3k 82 BC x BA yc yB za zB zc 2B Ya YB i 2c zB 4 B 10 eB Za 2B J ze zB YA YB yc yB ta amp B k pai psj pek p LA P2P5 P3P6 U IRo vi pP tp pr V pa ine Vips tpa Vies MOR V Pi 3 3 y pitoi Pe 7 E 3 1 2 pj p5 p 9 2p4 V pa 2p5 V ps 2p6 V ps a prats 1 2 p 3 p3 00 2pi V p1 2p2 Viv 2ps V ps for atom A ownd Gt atoms B C amp D fixed V p1 0 0 7 0 0 7 0 0 E V p2 0 0 7 0 0 7 0 0 E V p3 0 0 7 0 0 7 0 0 E V ps 0 0 2e zc F yc um k V ps zc 2B t 0 0 7 ep ac k V ps ye yo wo ap j 0 0 for atom B moving atoms A C amp D fixed V p1 0 0 zc zp j yo yc k V p2 20 20 1 0 0
17. 5771 5782 1998 C Simmerling M R Lee A R Ortiz A Kolinski J Skolnick and P A Kollman Com bining MONSSTER and LES PME to predict protein structure from amino acid sequence Application to the small protein CMTI 1 122 35 8392 8402 2000 T Straatsma and A McCammon Computational alchemy Ann Rev Phys Chem 43 407 435 1992 W F van Gunsteren Methods for calculation of free energies and binding constants successes and problems In W F Van Gunsteren and P K Weiner editors Computer simulation of biomolecular systems theoretical and experimental applications pages 27 59 ESCOM Science Publishers B V The Netherlands 1989 R W Zwanzig High temperature equation of state by a perturbation method i nonpolar gases J Chem Phys 22 1420 1426 1954 109 Index 1 4scaling parameter 46 alias psfgen command 34 37 amber parameter 23 ambercoor parameter 23 Atoms moving too fast 42 auto psfgen command 35 Bad global exclusion count 42 BerendsenPressure parameter 63 BerendsenPressureCompressibility parameter 64 BerendsenPressureFreq parameter 64 BerendsenPressureRelaxationTime parameter 64 BerendsenPressureTarget parameter 64 binaryoutput parameter 20 binaryrestart parameter 21 bincoordinates parameter 20 binvelocities parameter 20 BOUNDARY energy 22 callback command 15 cellBasisVectorl parameter 61 cellBasisVector2 parameter 61 cellBasisVector3 parameter 61 ce
18. Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee 8 Government Rights Because substantial governmental funds have been used in the devel opment of NAMD any possession use or sublicense of the Software by or to the United States government shall be subject to such required restrictions 9 NAMD is being distributed as a research and teaching tool and as such TBG encourages contributions from users of the code that might at Illinois sole discretion be used or incorporated to make the basic operating framework of the Software a more stable flexible and or useful product Licensees that wish to contribute their code to become an internal portion of the Software may be required to sign an Agreement Regarding Contributory Code for NAMD Software before Illinois can accept it contact namd ks uiuc edu for a copy Contact Information The best contact path for licensing issues is by e mail to namd ks uiuc edu or send correspondence to NAMD Team Theoretical Biophysics Group Beckman Institute University of Illinois 405 North Mathews MC 251 Urbana Illinois 61801 USA FAX 217 244 6078 Contents 1 Introduction 1 1 New features in version 2 5 oaoa ee 1 2 NAMD and molecular dynamics simulations 0 2 e o 1 3 User feedback 2
19. The number of the first timestep This value is typically used only when a simulation is a continuation of a previous simulation In this case rather than having the timestep restart at 0 a specific timestep number can be specified e stepspercycle lt timesteps per cycle gt Acceptable Values positive integer Default Value 20 Description Number of timesteps in each cycle Each cycle represents the number of timesteps between atom reassignments For more details on non bonded force evaluation see Section 5 1 5 3 2 Simulation space partitioning e cutoff lt local interaction distance common to both electrostatic and van der Waals calcu lations A gt Acceptable Values positive decimal Description See Section 5 1 for more information 43 e switching lt use switching function gt Acceptable Values on or off Default Value off Description If switching is specified to be off then a truncated cutoff is performed If switching is turned on then smoothing functions are applied to both the electrostatics and van der Waals forces For a complete description of the non bonded force parameters see Section 5 1 If switching is set to on then switchdist must also be defined e switchdist lt distance at which to activate switching function for electrostatic and van der Waals calculations A gt Acceptable Values positive decimal lt cutoff Description Distance at which the switching function should begin to take effect Th
20. Using this method all of the velocities in the system are periodically reassigned so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this reassignment is performed e reassignFreg lt number of timesteps between temperature reassignment gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the num ber of timesteps between each temperature reassignment If this value is given then the reassignTemp parameter must also be given to specify the target temperature e reassignTemp lt temperature for equilibration K gt Acceptable Values positive decimal Default Value temperature if set otherwise none Description The temperature to which all velocities will be reassigned every reassignFreq timesteps This parameter is valid only if reassignFreq has been set e reassignIncr lt temperature increment for equilibration K gt Acceptable Values decimal Default Value 0 Description In order to allow simulated annealing or other slow heating cooling protocols reassignIncr will be added to reassignTemp after each reassignment Reassignment is carried out at the first timestep The reassignHold parameter may be set to limit the final temperature This parameter is valid only if reassignFreq has been set e reassignHold lt holding temperature for equilibration K gt Acceptable Values positive decimal
21. VMD you can also use atom selections to write pieces of the structure to separate files Split a file containing protein and water into separate segments Creates files named myfile_water pdb myfile_frag0 pdb myfile_frag1 pdb Requires VMD mol load pdb myfile pdb set water atomselect top water water writepdb myfile_water pdb set protein atomselect top protein set chains lsort unique protein get pfragl foreach chain chains set sel atomselect top pfrag chain sel writepdb myfile_frag chain pdb 4 1 2 Deleting unwanted atoms The delatom command described below allows you to delete selected atoms from the structure It s fine to remove atoms from your structure before building the PSF and PDB files but you should never edit the PSF and PDB files created by psfgen by hand as it will probably mess up the internal numbering in the PSF file Very often the atoms you want to delete are water molecules that are either too far from the solute or else outside of the periodic box you are trying to prepare In either case VMD atom selections can be used to select the waters you want to delete For example Load a pdb and psf file into both psfgen and VMD resetpsf readpsf myfile psf readpdb myfile pdb mol load psf myfile psf pdb myfile pdb Select waters that are more than 10 Angstroms from the protein set badwater1 atomselect top name OH2 and not within 10 of protein 28 Alternatively select w
22. Value off Description Specifies whether or not cylindrical boundary conditions are to be applied to the system If set to on then cylindricalBCCenter cylindricalBCr1 cylindricalBC11 and cylindricalBCk1 must be defined and cylindricalBCAxis cylindricalBCexp1 cylindrica cylindricalBC12 cylindricalBCk2 and cylindricalBCexp2 can optionally be defined cylindricalBCCenter lt center of cylinder A gt Acceptable Values position Description Location around which cylinder is centered cylindricalBCAxis lt axis of cylinder A gt Acceptable Values x y or z Description Axis along which cylinder is aligned cylindricalBCr1 lt radius for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the non axis plane of the cylinder cylindricalBCl1 lt distance along cylinder axis for first boundary condition A gt Acceptable Values positive decimal Description Distance at which the first potential of the boundary conditions takes effect along the cylinder axis cylindricalBCk1 lt force constant for first potential gt Acceptable Values non zero decimal Description Force constant for the first harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center cylindricalBCexp1 lt exponent for first potential gt Acceptable Values posit
23. and Analysis There are several ways to apply external forces to simulations with NAMD These are described below 6 6 1 Constant Forces NAMD provides the ability to apply constant forces to some atoms There are two parameters that control this feature e constantforce lt Apply constant forces gt Acceptable Values yes or no Default Value no Description Specifies whether or not constant forces are applied e consforcefile lt PDB file containing forces to be applied gt Acceptable Values UNIX filename Description The X Y Z and occupancy O fields of this file are read to determine 66 the constant force vector of each atom which is X Y Z O in unit of kcal mol A The occupancy O serves as a scaling factor which could expand the range of the force applied One may be unable to record very large or very small numbers in the data fields of a PDB file due to limited space Zero forces are ignored Specifying consforcefile is optional constant forces may be specifed or updated between runs by using the consForceConfig command 6 6 2 External Electric Field NAMD provides the ability to apply a constant electric field to the molecular system being simu lated Energy due to the external field will be reported in the MISC column and may be discontin uous in simulations using periodic boundary conditions if for example a charged hydrogen group moves outside of the central cell There are two parameters that control
24. at any distance In this scheme the cutoff parameter has a slightly different meaning for the electrostatic interactions it represents the local interaction distance or distance within which electrostatic pairs will be directly calculated every timestep Outside of this distance interactions will be calculated only periodically These forces will be applied using a multiple timestep integration scheme as described in Section 5 2 2 direct at 5 every step ra o 0 distance Figure 3 Graph showing an electrostatic potential when full electrostatics are used within NAMD with one curve portion calculated directly and the other calculated using DPMTA 40 5 1 3 Nonbonded interaction distance testing The last critical parameter for non bonded interaction calculations is the parameter pairlistdist To reduce the cost of performing the non bonded interactions NAMD uses a non bonded pair list which contained all pairs of atoms for which non bonded interactions should be calculated Per forming the search for pairs of atoms that should have their interactions calculated is an expensive operation Thus the pair list is only calculated periodically at least once per cycle Unfortunately pairs of atoms move relative to each other during the steps between preparation of the pair list Because of this if the pair list were built to include only those pairs of atoms that are within the cutoff distance when the list is generated
25. between and may include multiple lines This parameter may occur multiple times and scripts will be executed in order of appearance The format of the free energy perturbation script is described below The following sections describe the format of the free energy perturbation script 6 7 1 User Supplied Conformational Restraints These restraints extend the scope of the available restraints beyond that provided by the harmonic position restraints Each restraint is imposed with a potential energy term whose form depends on the type of the restraint Fixed Restraints Position restraint 1 atom force constant K and reference position Tref E Kj 2 17 Pref Stretch restraint 2 atoms force constant Kf and reference distance drep E Ky 2 di dres Bend restraint 3 atoms force constant Ky and reference angle O E Ky 2 0 reg Torsion restraint 4 atoms energy barrier Eo and reference angle Xref E Eo 2 1 cos xi Xref Forcing restraints Position restraint 1 atom force constant Ky and two reference positions Tf and Tj E K 5 2 P Pref Tref AM 1 A T Stretch restraint 2 atoms force constant K f and two reference distances dy and d E Ky 2 di dref dref d 1 A do Bend restraint 3 atoms force constant K f and two reference angles 0o and 01 E K 1 2 0 Ores Oref AB 1 A Oo Torsion restraint 4 atoms energy barri
26. build a new configuration e loadcoords lt varname gt Loads requested atom and group coordinates in A into a local array loadcoords should only be called from within the calcforces procedure For example loadcoords p and print p 4 e loadforces lt varname gt Loads the forces applied in the previous timestep in kcal mol T into a local array loadforces should only be called from within the calcforces procedure For example loadforces f and print f 4 e loadtotalforces lt varname gt Loads the total forces on each requested atom in the previous time step in kcal mol A7 into a local array The total force also includes external forces Note that the loadforces command returns external forces applied by the user Therefore one can subtract the external force on an atom from the total force on this atom to get the pure force arising from the simulation system e loadmasses lt varname gt Loads requested atom and group masses in amu into a local array loadmasses should only be called from within the calcforces procedure For example loadcoords m and print m 4 e addforce lt atomid groupid gt lt force vector gt Applies force in kcal mol7 A to atom or group addforce should only be called from within the calcforces procedure For example addforce groupid 1 0 2 P e addenergy lt energy kcal mol gt This command adds the specified energy to the MIS
27. commercial use by individuals academic or research institutions and corporations for in house business purposes only upon completion and submission of the online registration form available from the NAMD web site http www ks uiuc edu Research namd Commercial use of the NAMD software or derivative works based thereon REQUIRES A COMMERCIAL LICENSE Commercial use includes 1 integration of all or part of the Software into a product for sale lease or license by or on behalf of Licensee to third parties or 2 distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee The University of Illinois will negotiate commercial use licenses for NAMD upon request These requests can be directed to namd ks uiuc edu Registration Individuals may register in their own name or with their institutional or corporate affiliations Registration information must include name title and e mail of a person with signature authority to authorize and commit the individuals academic or research institution or corporation as necessary to the terms and conditions of the license agreement All parts of the information must be understood and agreed to as part of completing the form Completion of the form is required before software access is granted Pay particular attention to the authorized requester requirements above and be sure that the form submission is authorized by the duly responsible pe
28. if one specifies some value for the force constant k in the PDB file effectively the force constant is 2k in calculations This caveat was removed in SMD feature The following parameters describe the parameters for the moving harmonic constraint feature of NAMD e movingConstraints lt Are moving constraints active gt Acceptable Values on or off 67 Default Value off Description Should moving restraints be applied to the system If set to on then movingConsVel must be defined May not be used with rotConstraints e movingConsVel lt Velocity of the reference position movement gt Acceptable Values vector in A timestep Description The velocity of the reference position movement Gives both absolute value and direction 6 6 4 Rotating Constraints The constraints parameters are specified in the same manner as for usual static harmonic con straints The reference positions of all constrained atoms are then rotated with a given angular velocity about a given axis If the force constant of the constraints is sufficiently large the con strained atoms will follow their reference positions A rotation matrix M about the axis unit vector v is calculated every timestep for the angle of rotation corresponding to the current timestep angle Qt where Q is the angular velocity of rotation From now on all quantities are 3D vectors except the matrix M and the force constant K The current reference position R is calculated from t
29. insulin 10 cg kf 20 ref 6 2 dihe group ca insulin 10 to insulin 12 group ca cb cg insulin 15 to insulin 18 group insulin 20 insulin 22 group ca insulin 30 to insulin 32 insulin 34 all insulin 35 barr 20 ref 90 Bound specifications 1 impose an upper bound if an atom s position strays too far from a reference position add an energy term if the atom is more than 10A from 2 0 2 0 2 0 2823 impose lower and upper bounds on the distance between the ca s of residues 5 and 15 if the separation is less than 5 0A or greater than 12 0A add an energy term 4 impose a lower bound on the angle between the centers of mass of residues 3 6 9 if the angle goes lower than 90 apply a restraining potential urestraint posi bound insulin 3 cb kf 20 hi 2 0 2 0 2 0 10 0 dist bound insulin 5 ca insulin 15 ca kf 20 low 5 0 dist bound insulin 5 ca insulin 15 ca kf 20 hi 12 0 angle bound insulin 3 insulin 6 insulin 9 kf 20 low 90 0 torsional bounds are defined as pairs this example specifies upper and lower bounds on the dihedral angle X separating the planes of the 1 2 3 residues and the 2 3 4 residues The energy is 0 for 90 jx 120 The energy is 20 kcal mol for 130 jx j 260 Energy rises from 0 20 kcal mol as X increases from 120 130 and decreases from 90 100 urestraint
30. is active e pairInteractionFile lt PDB file containing pair interaction flags gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to specify atoms to use for pair interaction calculations If this 89 parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used pairInteractionCol lt column of PDB file containing pair interaction flags gt Acceptable Values X Y Z 0 or B Default Value B Description Column of the PDB file to specify which atoms to use for pair interaction calculations This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling pairInteractionSelf lt compute within group interactions instead of bewteen groups gt Acceptable Values on or off Default Value off Description When active NAMD will compute bonded and nonbonded interactions only for atoms within group 1 pairInteractionGroup1 lt Flag to indicate atoms in group 1 gt Acceptable Values integer Description pairInteractionGroup2 lt Flag to indicate atoms in group 2 gt Acceptable Values integer Description These options are used to indicate which atoms belong to each interac tion group Atoms with a value in the column specified by pairInteractionCol equal to pairInteractionGroup1 will be assigned to group 1 likewise for group 2 6 11 Pressure Profile Calcul
31. of Figures oP WN rH Graph of van der Waals potential with and without switching 39 Graph of electrostatic potential with and without shifting function 40 Graph of electrostatic split between short and long range forces 40 Example of cutoff and pairlist distance uses 2 2 ee ee 42 Dual topology description for an alchemical simulation Case example of the muta tion of alanine into glycine The lighter color denotes the non interacting alternate 1 Introduction NAMD is a parallel molecular dynamics program for UNIX platforms designed for high performance simulations in structural biology This document describes how to use NAMD its features and the platforms on which it runs The document is divided into several sections Section 1 gives an overview of NAMD Section 2 lists the basics for getting started Section 3 describes NAMD file formats Section 4 explains PSF file generation with psfgen Section 5 lists basic simulation options Section 6 lists additional simulation options Section 7 provides hints for X PLOR users Section 8 provides sample configuration files Section 9 gives details on running NAMD Section 10 gives details on installing NAMD We have attempted to make this document complete and easy to understand and to make NAMD itself easy to install and run We welcome your suggestions for improving the documentation or code at namd ks uiuc edu 1 1 New features in ver
32. of binding affinities a critical review Biophys J 72 1047 1069 1997 W Humphrey and A Dalke VMD user guide Version 0 94 Beckman Institute Technical Report TB 94 07 University of Illinois 1994 P M King Free energy via molecular simulation A primer In W F van Gunsteren P K Weiner and A J Wilkinson editors Computer simulation of biomolecular systems Theoretical and experimental applications volume 2 pages 267 314 ESCOM Leiden 1993 P A Kollman Free energy calculations applications to chemical and biochemical phenomena Chem Rev 93 2395 2417 1993 A E Mark Free energy perturbation calculations In P Schleyer editor Encyclopaedia of computational chemistry volume 2 pages 1070 1083 John Wiley and Sons New York 1998 J A McCammon and S C Harvey Dynamics of Proteins and Nucleic Acids Cambridge University Press Cambridge 1987 D A Pearlman A comparison of alternative approaches to free energy calculations J Phys Chem 98 1487 1493 1994 108 16 17 18 19 20 21 A Roitberg and R Elber Modeling side chains in peptides and proteins Application of the locally enhanced sampling technique and the simulated annealing methods to find minimum energy conformations 95 9277 9287 1991 C Simmerling T Fox and P A Kollman Use of locally enhanced sampling in free energy calculations Testing and application to the a 8 anomerization of glucose 120 23
33. of copies created for enhanced atoms The enhanced atoms may be easily observed in VMD with the atom selection beta 0 6 9 2 Simulation In practice LES is a simple method used to increase sampling no special output is generated The following parameters are used to enable LES e les lt is locally enhanced sampling active gt Acceptable Values on or off Default Value off Description Specifies whether or not LES is active 88 e lesFactor lt number of LES images to use gt Acceptable Values positive integer equal to the number of images present Description This should be equal to the factor used in multiply when creating the structure The interaction potentials for images is divided by lesFactor e lesFile lt PDB file containing LES flags gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to specify the LES image number of each atom If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used e lesCol lt column of PDB file containing LES flags gt Acceptable Values X Y Z 0 or B Default Value B Description Column of the PDB file to specify the LES image number of each atom This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling A value of 0 in this column indicates that the atom is not enhanced Any other value should be a posit
34. perturbation FEP 21 4 20 19 12 9 13 8 within NAMD has now been implemented In FEP the free energy difference between two states a and b is expressed by AAaso kBT In exp Hole p melep 3 kgT a wherein kg is the Boltzmann constant T is the temperature and H r p and H r p are the Hamiltonians characteristic of states a and b respectively denotes an ensemble average over configurations representative of the initial state a In practice the transformation between the two thermodynamic states is replaced by a series of transformations between non physical intermediate states along a pathway that connects a to b This pathway is characterized by a variable referred to as coupling parameter 4 13 11 A that makes the free energy a continuous function of this parameter between a and b N H r P Arti H r p e AA kgT Y 1 4 b B 2 n exp kpT 4 Here N stands for the number of intermediate states or windows between the initial and the final states In a typical FEP setup that involves the transformation of one chemical species into another one the atoms in the molecular topology can be separated into three groups i a group of atoms that do not change during the simulation e g the environment ii those atoms describing the initial state a of the system and iii those that correspond to the final state b at the end of the alchemical transformation
35. specified by coordinates is used e tCoupleCol lt column of PDB from which to read coefficients gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for the temperature coupling coefficient for each atom This value can be read from any floating point column of the PDB file A value of 0 indicates that the atom will remain unaffected 6 3 3 Temperature rescaling parameters NAMD allows equilibration of a system by means of temperature rescaling Using this method all of the velocities in the system are periodically rescaled so that the entire system is set to the desired temperature The following parameters specify how often and to what temperature this rescaling is performed e rescaleFreq lt number of timesteps between temperature rescaling gt Acceptable Values positive integer Description The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature rescaling If this value is given then the rescaleTemp parameter must also be given to specify the target temperature 57 e rescaleTemp lt temperature for equilibration K gt Acceptable Values positive decimal Description The temperature to which all velocities will be rescaled every rescaleFreq timesteps This parameter is valid only if rescaleFreq has been set 6 3 4 Temperature reassignment parameters NAMD allows equilibration of a system by means of temperature reassignment
36. steps so that A is fixed while dU dA is accumulated Lamba control for slow growth pmf task up down stop grow fade or nogrow time T fs ps or ns default ps lambda Y value of A only needed for stop and nogrow lambdat Z value of A only needed for grow fade and nogrow default 0 print P fs ps or ns or noprint default ps up down stop A is applied to the reference values grow fade nogrow A is applied to Ky A fixed value Az is used to determine the ref values up grow A changes from 0 1 no value of A is required down fade A changes from 1 0 no value of A is required stop nogrow dU dA is accumulated for single point MCTI Lambda control for automated MCTI meti task stepup stepdown stepgrow or stepfade equiltime T1 fs ps or ns default ps accumtime T2 fs ps or ns default ps numsteps N lambdat Z value of A only needed for stepgrow and stepfade default 0 print P fs ps or ns or noprint default ps stepup stepdown A is applied to the reference values stepgrow stepfade A is applied to Ky A fixed value A is used to determine the ref values stepup stepgrow A changes from 0 gt 1 no value of A is required stepdown stepfade A changes from 1 gt 0 no value of A is required For each task A changes in steps of 1 0 N from 0 gt 1 or 1 gt 0 At each step no data is accumulated for the init
37. the same file for future use This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file FFTWWisdomFile lt name of file for FFTW wisdom archive gt Acceptable Values file name Default Value FFTW_NAMD_version_platform txt Description File where FFTW wisdom is read and saved If you only run on one platform this may be useful to reduce startup times for all runs The default is likely sufficient as it is version and platform specific useDPME lt Use old DPME code gt Acceptable Values yes or no Default Value no Description Switches to old DPME implementation of particle mesh Ewald The new code is faster and allows non orthogonal cells so you probably just want to leave this option turned off If you set cell0rigin to something other than 0 0 0 the energy may differ slightly between the old and new implementations DPME is no longer included in released binaries 5 3 6 Full direct parameters The direct computation of electrostatics is not intended to be used during real calculations but rather as a testing or comparison measure Because of the O N computational complexity for performing direct calculations this is much slower than using DPMTA or PME to compute full electrostatics for large systems In the case of periodic boundary conditions the nearest image convention is used rather than a full Ewald sum e FullDirect lt calculate full
38. timestep e Input and Output Compatibility The input and output file formats used by NAMD are identical to those used by CHARMM 11 and X PLOR Input formats include coordinate files in PDB format 3 structure files in X PLOR PSF format and energy parameter files in either CHARMM or X PLOR formats Output formats include PDB coordinate files and binary DCD trajectory files These similar ities assure that the molecular dynamics trajectories from NAMD can be read by CHARMM or X PLOR and that the user can exploit the many analysis algorithms of the latter packages e Dynamics Simulation Options MD simulations may be carried out using several options including Constant energy dynamics Constant temperature dynamics via x Velocity rescaling Velocity reassignment Langevin dynamics Periodic boundary conditions Constant pressure dynamics via x Berendsen pressure coupling Nos Hoover Langevin piston Energy minimization Fixed atoms Rigid waters Rigid bonds to hydrogen Harmonic restraints Spherical or cylindrical boundary restraints e Easy to Modify and Extend Another primary design objective for NAMD is extensibility and maintainability In order to achieve this it is designed in an object oriented style with C Since molecular dynam ics is a new field new algorithms and techniques are continually being developed NAMD s modular design allows one to integrate and
39. to ignore explicit exclusions is not present within NAMD thus only positive values of NBXMod have NAMD equivalents These equivalences are NBXMod 1 is equivalent to exclude none no atom pairs excluded NBXMod 2 is equivalent to exclude 1 2 only 1 2 pairs excluded NBXMod 3 is equivalent to exclude 1 3 1 2 and 1 3 pairs excluded NBXMod 4 is equivalent to exclude 1 4 1 2 1 3 and 1 4 pairs excluded NBXMod 5 is equivalent to exclude scaled1 4 1 2 and 1 3 pairs excluded 1 4 pairs modified 93 NAMD Parameter switching X PLOR Parameter SHIFt VSWItch and TRUNcation Activating the NAMD option switching is equivalent to using the X PLOR options SHIFt and VSWItch Deactivating switching is equivalent to using the X PLOR option TRUNcation NAMD Parameter temperature X PLOR Parameter FIRSttemp Initial temperature for the system NAMD Parameter rescaleFreq X PLOR Parameter IEQFrq Number of timesteps between velocity rescaling NAMD Parameter rescaleTemp X PLOR Parameter FINAltemp Temperature to which velocities are rescaled NAMD Parameter restartname X PLOR Parameter SAVE Filename prefix for the restart files NAMD Parameter restartfreq X PLOR Parameter ISVFrq Number of timesteps between the generation of restart files NAMD Parameter DCDfile X PLOR Parameter TRAJectory Filename for the position trajectory file NAMD Parameter DCDfreq X PLOR Parameter NSAVC Numbe
40. van der Waals interactions 004 5 1 2 Non bonded electrostatic interactions o e e 5 1 3 Nonbonded interaction distance testing e 5 2 Full electrostatic integration ee 5 3 NAMD configuration parameters 2 0 ee 5 3 1 Timestep parameters 5 3 2 Simulation space partitioning e 53 30 Basic dynAmiCS air ai A a E E 5 3 4 DPMTA parameters 2 0 0 0 0 ee ee ee 10 10 11 13 13 14 14 14 14 15 16 18 18 18 18 18 18 19 19 20 22 23 25 27 27 28 28 29 33 34 530 PME parameters air A Oa Ae ase ba at PSS es 49 5 3 6 Full direct parameters 2 0 a 50 5 3 7 Multiple timestep parameters 0 0 2 0000 eee eee ee 51 6 Additional Simulation Parameters 53 6 1 Constraints and Restraints ee 53 6 1 1 Harmonic constraint parameters 0 0 0 0 ee eee 53 6 1 2 Fixed atoms parameters 2 0002 eee ee ee eee 54 6 2 bn rey Minimization sosete p manyin rr RAE 55 6 2 1 Conjugate gradient parameters 55 6 2 2 Velocity quenching parameters a 55 6 3 Temperature Control and Equilibration o oaoa a 56 6 3 1 Langevin dynamics parameters 56 6 3 2 Temperature coupling parameters a 57 6 3 3 Temperature rescaling parameters a 57 6 3 4 Temperature reassignment parameters e o 58 6 4 Boundary Conditions ooo a 58 6 4 1 Spherical harmonic bounda
41. window before data collection gt Acceptable Values positive integer less than numSteps or run Default Value 0 Description In each window fepEquilSteps steps of equilibration can be performed before ensemble averaging is initiated The output also contains the data gathered during equilibration and is meant for analysis of convergence properties of the FEP calculation e fepFile lt pdb file with perturbation flags gt Acceptable Values filename Default Value coordinates Description pdb file to be used for indicating the FEP status for each of the atoms pertaining to the system If this parameter is not declared specifically then the pdb file containing the initial coordinates specified by coordinates is utilized for this information e fepCol lt Column in the fepFile that carries the perturbation flag gt Acceptable Values X Y Z O or B Default Value B Description Column of the pdb file to use for retrieving the FEP status of each atom e a flag that indicates which atom will be perturbed in the course of the simulation A value of 1 in the specified column indicates the atom will vanish during the FEP calculation whereas a value of 1 indicates that the atom will grow e fepOutFreq lt Frequency of FEP energy output in time steps gt Acceptable Values positive integer Default Value 5 86 Description Every fepOutFreq number of MD steps the output file fepOutFile is updated by dumping energies that are used for en
42. yes or no Default Value yes Description PARM file explicitly gives complete exclusion including 1 4 exclusions information When readexclusions is set to on NAMD will read all exclusions from PARM file and will not add any more alternatively if readexclusions is set to off NAMD will ignore the exclusions in PARM file and will automatically generate them according to the exclusion policy specified by exclude e scnb lt VDW 1 4 scaling factor gt Acceptable Values decimal gt 1 0 Default Value 2 0 Description Same meaning as SCNB in AMBER Note that in NAMD 1 4 vdw inter actions are DIVIDED by scnb whereas 1 4 electrostatic interactions are MULTIPLIED by 1 4scaling So 1 4scaling should be set to the inverse of SCEE value used in AMBER Caveat 1 Polarizable parameters in AMBER are not supported 2 NAMD does not support the 10 12 potential terms in some old AMBER versions When non zero 10 12 parameter is encountered in PARM file NAMD will terminate 3 NAMD has several exclusion policy options defined by exclude The way AMBER dealing with exclusions corresponds to the scaled1 4 in NAMD So for simulations using AMBER force field one would specify exclude scaled1 4 in the configuration file and set 1 4scaling to the inverse value of SCEE as would be used in AMBER 23 4 NAMD does not read periodic box lengths in PARM or coordinate file They must be explicitly specified in NAMD configuration file 5 By d
43. 2 parameter files NAMD supports CHARMM19 and CHARMM22 parameter files in both X PLOR and CHARMM formats X PLOR format is the default CHARMM format parameter files may be used given the parameter paraTypeCharmm on For a full description of the format of commands used in these files see the X PLOR and CHARMM User s Manual 7 3 1 4 DCD trajectory files NAMD produces DCD trajectory files in the same format as X PLOR and CHARMM The DCD files are single precision binary FORTRAN files so are transportable between computer architec tures They are not unfortunately transportable between big endian most workstations and little endian Intel architectures This same caveat applies to binary velocity and coordinate files The utility programs flipdcd and flipbinpdb are provided with the Linux Intel version to reformat these files The exact format of these files is very ugly but supported by a wide range of analysis and display programs 18 3 2 NAMD configuration parameters 3 2 1 Input files coordinates lt coordinate PDB file gt Acceptable Values UNIX filename Description The PDB file containing initial position coordinate data Note that path names can be either absolute or relative Only one value may be specified structure lt PSF file gt Acceptable Values UNIX filename Description The X PLOR format PSF file describing the molecular system to be simu lated Only one value may be specified paramet
44. B and atom B is bonded to atom C and atom C is bonded to atom D then the atom pair A D would be excluded With the value of scaled1 4 all 1 3 pairs are excluded and all pairs that match the 1 4 criteria are modified The electrostatic interactions for such pairs are modified by the constant factor defined by 1 4scaling The van der Waals interactions are modified by using the special 1 4 parameters defined in the parameter files e temperature lt initial temperature K gt Acceptable Values positive decimal Description Initial temperature value for the system Using this option will generate a random velocity distribution for the initial velocities for all the atoms such that the system is at the desired temperature Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e COMmotion lt allow center of mass motion gt Acceptable Values yes or no Default Value no Description Specifies whether or not motion of the center of mass of the entire system is allowed If this option is set to no the initial velocities of the system will be adjusted to remove center of mass motion of the system Note that this does not preclude later center of mass motion due to external forces such as random noise in Langevin dynamics boundary potentials and harmonic restraints e dielectric lt dielectric constant for system gt Acceptable Values
45. C column and hence the total energy in the energy output For normal runs the command does not affect the simulation trajectory at all and only has an artificial effect on its energy output However it can indeed affect minimizations With the commands above and the functionality of the Tcl language one should be able to perform any on the fly analysis and manipulation To make it easier to perform certain tasks some Tcl routines are provided below 72 Several vector routines vecadd vecsub vecscale from the VMD Tcl interface are defined Please refer to VMD manual for their usage The following routines take atom coordinates as input and return some geometry parameters bond angle dihedral e getbond lt coori gt lt coor2 gt Returns the length of the bond between the two atoms Actually the return value is simply the distance between the two coordinates coorl and coor2 are coordinates of the atoms e getangle lt coor1 gt lt coor2 gt lt coor3 gt Returns the angle from 0 to 180 defined by the three atoms coor1 coor2 and coor3 are coordinates of the atoms e getdihedral lt coori gt lt coor2 gt lt coor3 gt lt coor4 gt Returns the dihedral from 180 to 180 defined by the four atoms coorl coor2 coor3 and coor4 are coordinates of the atoms The following routines calculate the derivatives gradients of some geometry parameters angle dihedral e
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47. NAMD will typically consist of the following steps 1 Preparing separate PDB files containing individual segments of protein solvent etc before running psfgen 2 Reading in the appropriate topology definition files and aliasing residue and atom names found in the PDB file to those found in the topology files This will generally include selecting a default protonation state for histidine residues 3 Generating the default structure using segment and pdb commands 4 Applying additional patches to the structure 5 Reading coordinates from the PDB files 27 6 Deleting unwanted atoms such as overlapping water molecules 7 Guessing missing coordinates of hydrogens and other atoms 8 Writing PSF and PDB files for use in NAMD 4 1 1 Preparing separate PDB files Many PDB files in the PDB databank contain multiple chains corresponding to protein subunits water and other miscellaneous groups Protein subunits are often identified by their chain ID in the PDB file In psfgen each of these groups must be assigned to their own segment This applies most strictly in the case of protein chains each of which must be assigned to its own segment so that N terminal and C terminal patches can be applied You are free to group water molecules into whatever segments you choose Chains can be split up into their own PDB files using your favorite text editor and or Unix shell commands as illustrated in the BPTI example below If you are using
48. SC in the energy output addenergy expr k phi phi 2 0 Calculate the force along the dihedral according to the harmonic constraint set force expr k phi Calculate the gradients foreach g1 g2 g3 g4 dihedralgrad p aid1 p aid2 p aid3 p aid4 The force to be applied on each atom is proportional to its corresponding gradient addforce aid1 vecscale g1 force addforce aid2 vecscale g2 force addforce aid3 vecscale g3 force addforce aid4 vecscale g4 force 6 7 Free Energy of Conformational Change Calculations NAMD incorporates methods for performing free energy of conformational change perturbation calculations The system is efficient if only a few coordinates either of individual atoms or centers of mass of groups of atoms are needed The following configuration parameters are used to enable free energy perturbation e freeEnergy lt is free energy perturbation active gt Acceptable Values on or off Default Value off Description Specifies whether or not free energy perturbation is active If it is set to off then no free energy perturbation is performed If it is set to on then the free energy perturbation calculation specified in freeEnergyConfig parameters is executed e freeEnergyConfig lt free energy perturbation script gt Acceptable Values file or script 74 Description Must contain either the name of a free energy perturbation script file or the script itself
49. Value off Description Restrain the Cartesian z components of the positions 6 1 2 Fixed atoms parameters Atoms may be held fixed during a simulation NAMD avoids calculating most interactions in which all affected atoms are fixed unless fixedAtomsForces is specified e fixedAtoms lt are there fixed atoms gt Acceptable Values on or off Default Value off Description Specifies whether or not fixed atoms are present e fixedAtomsForces lt are forces between fixed atoms calculated gt Acceptable Values on or off Default Value off Description Specifies whether or not forces between fixed atoms are calculated This option is required for constant pressure or to turn fixed atoms off in the middle of a simulation e fixedAtomsFile lt PDB file containing fixed atom parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the fixed atom flags for each atom If this parameter is not specified then the PDB file specified by coordinates is used e fixedAtomsCol lt column of PDB containing fixed atom parameters gt Acceptable Values X Y Z 0 or B 54 Default Value 0 Description Column of the PDB file to use for the containing fixed atom parameters for each atom The coefficients can be read from any floating point column of the PDB file A value of 0 indicates that the atom is not fixed 6 2 Energy Minimization 6 2 1 Conjugate gradient parameters The default minimi
50. Y Z 0 or B 56 Default Value 0 Description Column of the PDB file to use for the Langevin coupling coefficients for each atom The coefficients can be read from any floating point column of the PDB file A value of 0 indicates that the atom will remain unaffected 6 3 2 Temperature coupling parameters NAMD is capable of performing temperature coupling in which forces are added or reduced to simulate the coupling of the system to a heat bath of a specified temperature This capability is based on that implemented in X PLOR which is detailed in the X PLOR User s Manual 7 e tCouple lt perform temperature coupling gt Acceptable Values on or off Default Value off Description Specifies whether or not temperature coupling is active If set to on then the parameter tCoupleTemp must be set and the parameters tCoupleFile and tCoupleCol can optionally be set to control the behavior of this feature e tCoupleTemp lt temperature for heat bath K gt Acceptable Values positive decimal Description Temperature to which atoms affected by temperature coupling will be ad justed This temperature will be roughly maintained across the affected atoms through the addition of forces e tCoupleFile lt PDB file with tCouple parameters gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for the temperature coupling coefficient for each atom If this parameter is not specified then the PDB file
51. ajectory output file gt Acceptable Values UNIX filename Description The binary DCD velocity trajectory filename This file stores the trajectory of all atom velocities using the same format binary DCD as X PLOR If velDCDfile is defined then velDCDfreq must also be defined velDCDfreq lt timesteps between writing velocities to trajectory file gt Acceptable Values positive integer 21 Description The number of timesteps between the writing of velocities to the trajectory file The initial velocities will not be included in the trajectory file 3 2 3 Standard output NAMD logs a variety of summary information to standard output The standard units used by NAMD are Angstroms for length kcal mol for energy Kelvin for temperature and bar for pressure Wallclock or CPU times are given in seconds unless otherwise noted BOUNDARY energy is from spherical boundary conditions and harmonic restraints while MISC energy is from external electric fields and various steering forces TOTAL is the sum of the various potential energies and the KINETIC energy TOTAL2 uses a slightly different kinetic energy that is better conserved during equilibration in a constant energy ensemble TOTAL3 is another variation with much smaller short time fluctuations that is also adjusted to have the same running average as TOTAL2 Defects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2 PRESSURE is the pressure calcula
52. ally the packages X PLOR 7 and CHARMM 6 To achieve this compatibility the set of input files which NAMD uses to define a molecular system are identical to the input files used by X PLOR and CHARMM Thus it is trivial to move an existing simulation from X PLOR or CHARMM to NAMD A description of these molecular system definition files is given in Section 3 1 In addition the output file formats used by NAMD were chosen to be compatible with X PLOR and CHARMM In this way the output from NAMD can be analyzed using X PLOR CHARMM or a variety of the other tools that have been developed for the existing output file formats Descriptions of the output files formats are also given in Section 3 1 3 1 File formats 3 1 1 PDB files The PDB Protein Data Bank format is used to store coordinate or velocity data being input or output from NAMD This is the standard format for coordinate data for most other molecular dynamics programs as well including X PLOR and CHARMM A full description of this file for mat can be obtained via anonymous FTP from ftp pdb bnl1 gov in pub format desc ps Z or pub format desc txt 3 1 2 X PLOR format PSF files NAMD uses the same protein structure files that X PLOR does At this time the easiest way to generate these files is using X PLOR or CHARMM although it is possible to build them by hand CHARMM can generate an X PLOR format PSF file with the command write psf card xplor 3 13 CHARMM19 and CHARMM2
53. alues nonnegative integer Default Value 0 Description The number of timesteps between each timing output of NAMD If specified and nonzero CPU and wallclock times will be output to stdout These data are from node 0 only CPU times for other nodes may vary 22 3 3 AMBER force field parameters AMBER format PARM file and coordinate file can be read by NAMD which allows one to use AMBER force field to carry out all types of simulations that NAMD has supported NAMD can read PARM files in either the format used in AMBER 6 or the new format defined in AMBER 7 The output of the simulation restart file DCD file etc will still be in traditional format that has been used in NAMD e amber lt use AMBER format force field gt Acceptable Values yes or no Default Value no Description If amber is set to on then parmfile must be defined and structure and parameters should not be defined e parmfile lt AMBER format PARM file gt Acceptable Values UNIX filename Description This file contains complete topology and parameter information of the system e ambercoor lt AMBER format coordinate file gt Acceptable Values UNIX filename Description This file contains the coordinates of all the atoms Note that coordinates can also be used for PDB format coordinate file When amber is set to on either ambercoor or coordinates must be defined but not both e readexclusions lt Read exclusions from PARM file gt Acceptable Values
54. amics functions that X PLOR provides As such there are many similarities between the types of parameters that must be passed to both X PLOR and NAMD This section describes relations between similar NAMD and X PLOR parameters e NAMD Parameter cutoff X PLOR Parameter CTOFNB When full electrostatics are not in use within NAMD these parameters have exactly the same meaning the distance at which electrostatic and van der Waals forces are truncated When full electrostatics are in use within NAMD the meaning is still very similar The van der Waals force is still truncated at the specified distance and the electrostatic force is still computed at every timestep for interactions within the specified distance However the NAMD integration uses multiple time stepping to compute electrostatic force interactions beyond this distance every stepspercycle timesteps e NAMD Parameter vdwswitchdist X PLOR Parameter CTONNB Distance at which the van der Waals switching function becomes active e NAMD Parameter pairlistdist X PLOR Parameter CUTNb Distance within which interaction pairs will be included in pairlist e NAMD Parameter 1 4scaling X PLOR Parameter E14Fac Scaling factor for 1 4 pair electrostatic interactions e NAMD Parameter dielectric X PLOR Parameter EPS Dielectric constant e NAMD Parameter exclude X PLOR Parameter NBXMod Both parameters specify which atom pairs to exclude from non bonded interactions The ability
55. and how ShakeH is used gt Acceptable Values none water all Default Value none Description When rigidBonds is all the bond between each hydrogen and its mother atom is fixed to the nominal bond length given in the parameter file When water is selected only the bonds between the hydrogens and the oxygen in water molecules are constrained For the default case none no lengths are constrained rigidTolerance lt allowable bond length error for ShakeH A gt Acceptable Values positive decimal Default Value 1 0e 8 Description The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount rigidIterations lt maximum ShakeH iterations gt Acceptable Values positive integer Default Value 100 Description The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths If the bond lengths do not converge a warning message is printed and the atoms are left at the final value achieved by ShakeH Although the default value is 100 convergence is usually reached after fewer than 10 iterations rigidDieOnError lt maximum ShakeH iterations gt Acceptable Values on or off Default Value on Description Exit and report an error if rigidTolerance is not achieved after rigidItera tions useSettle lt Use SETTLE for waters gt Acceptable Values on or off Default Value on Description If rigidBonds ar
56. anglegrad lt coor1 gt lt coor2 gt lt coor3 gt An angle defined by three atoms is a function of their coordinates 0 71 73 73 in radian This command takes the coordinates of the three atoms as input and returns a list of oe oe Each element of the list is a 3 D vector in the form of a Tcl list e dihedralgrad lt coor1 gt lt coor2 gt lt coor3 gt lt coor4 gt A dihedral defined by four atoms is a function of their coordinates ri 7 73 74 in radian This command takes the coordinates of the four atoms as input and returns a list of ge oe 2 oe Each element of the list is a 3 D vector in the form of a Tcl list As an example here s a script which applies a harmonic constraint reference position being 0 to a dihedral Note that the addenergy line is not really necessary it simply adds the calculated constraining energy to the MISC column which is displayed in the energy output tclForcesScript The IDs of the four atoms defining the dihedral set aidi 112 set aid2 123 set aid3 117 set aid4 115 The spring constant for the harmonic constraint set k 3 0 addatom aid1 addatom aid2 addatom aid3 addatom aid4 73 set PI 3 1416 proc calcforces 1 global aidi aid2 aid3 aid4 k PI loadcoords p Calculate the current dihedral set phi getdihedral p aid1 p aid2 p aid3 p aid4 Change to radian set phi expr phix PI 180 optional Add this constraining energy to MI
57. ast lt patch name gt Purpose Override default patch applied to last residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments residue lt resid gt lt resname gt Purpose Add a single residue to the end of the current segment Arguments lt resid gt Unique name for residue 1 5 characters usually numeric lt resname gt Residue type name from topology file Context Anywhere within segment pdb lt file name gt Purpose Extract sequence information from PDB file when building segment Residue IDs will be preserved residue names must match entries in the topology file or should be aliased before pdb is called Arguments lt file name gt PDB file containing known or aliased residues Context Anywhere within segment mutate lt resid gt lt resname gt Purpose Change the type of a single residue in the current segment Arguments lt resid gt Unique name for residue 1 5 characters usually numeric lt resname gt New residue type name from topology file Context Within segment after target residue has been created patch lt patch residue name gt lt segid resid gt Purpose Apply a patch to one or more residues Patches make small modifications to the structure of residues such as converting one to a terminus changing the protonation state
58. ate with NAMD to freely distribute such complimentary works and to direct others to the TBG server to obtain copies of NAMD itself 2 Licensee may at its own expense modify the Software to make derivative works for its own academic research and internal business purposes Licensee s distribution of any derivative work is also subject to the same restrictions on distribution and use limitations that are specified herein for Illinois Software Prior to any such distribution the Licensee shall require the recipient of the Licensee s derivative work to first execute a license for NAMD with Illinois in accordance with the terms and conditions of this Agreement Any derivative work should be clearly marked and renamed to notify users that it is a modified version and not the original NAMD code distributed by Illinois 3 Except as expressly set forth in this Agreement THIS SOFTWARE IS PROVIDED AS IS AND ILLINOIS MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO WARRANTIES OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT TRADE MARK OR OTHER RIGHTS LICENSEE ASSUMES THE ENTIRE RISK AS TO THE RE SULTS AND PERFORMANCE OF THE SOFTWARE AND OR ASSOCIATED MATERIALS LICENSEE AGREES THAT UNIVERSITY SHALL NOT BE HELD LIABLE FOR ANY DI RECT INDIRECT CONSEQUENTIAL OR INCIDENTAL DAMAGES WITH RESPECT TO ANY C
59. aters that are outside our periodic cell set badwater2 atomselect top name OH2 and x lt 30 or x gt 30 or y lt 30 or gt 30 or z lt 30 or z gt 30 Delete the residues corresponding to the atoms we selected foreach segid badwater1 get segid resid badwater1 get resid delatom segid resid Have psfgen write out the new psf and pdb file VMD s structure and coordinates are unmodified writepsf myfile_chopwater psf writepdb myfile_chopwater pdb 4 2 BPTI Example To actually run this demo requires e the program psfgen from any NAMD distribution e the CHARMM topology and parameter files top_al122_prot inp and par_a1122_prot inp from https rxsecure umaryland edu research amackere research html and e the BPTI PDB file 6PTI pdb available from the Protein Data Bank at http www pdb org by searching for 6PTI and downloading the complete structure file in PDB format Building the BPTI structure In this demo we create the files bpti psf and bpti pdb in the output directory which can then be used for a simple NAMD simulation File bpti_example tcl Requirements topology file top_al122_prot inp in directory toppar PDB file 6PTI pdb in current directory Create working directory remove old output files mkdir p output rm f output 6PTI_protein pdb output 6PTI_water pdb 1 Split input PDB file into segments grep v HETATM 6PTI pdb gt output 6PTI_protein pdb grep HOH 6PTI pdb g
60. ations NAMD supports the calculation of lateral pressure profiles as a function of the z coordinate in the system The algorithm is essentially that described by Lindahl and Edholm The simulation space is partitioned into slabs and the virial due to the interaction between two particles is distributed across the slabs containing the particles as well as the slabs that lie between the particles taking periodic boundary conditions into account The diagonal components of the pressure tensor for each slab are recorded in the NAMD output file The units of pressure are the same as in the regular NAMD pressure output i e bar The total virial contains contributions from three components kinetic energy bonded interac tions and nonbonded interactions The kinetic and bonded components are easily calculated every timestep and thus may be computed during a normal simulation run The nonbonded component however adds significant overhead and has not been implemented for PME cal culations The calculation of the nonbonded contribution should be performed offline using the saved frames of the trajectory file and a long nonbonded cutoff Pressure profile calculations may be performed in either constant volume or constant pressure conditions If constant pressure is enabled the slabs thickness will be rescaled along with the unit cell the dcdUnitCell option will also be switched on so that unit cell information is stored in the trajectory file Pe
61. ault orientation Write structure and coordinate files Now that all of the atoms and bonds have been created we can write out the psf structure file for the system We also create the matching coordinate pdb file The psf and pdb files are a matched set with identical atom ordering as needed by NAMD Using generated files in NAMD The files bpti pdb and bpti psf can now be used with NAMD but the initial coordinates require minimization first The following is an example NAMD configuration file for the BPTI example 31 NAMD configuration file for BPTI molecular system structure output bpti psf force field paratypecharmm on parameters toppar par_all22_prot inp exclude scaledi 4 1 4scaling 1 0 approximations switching on switchdist 8 cutoff 12 pairlistdist 13 5 margin 0 stepspercycle 20 integrator timestep 1 0 output outputenergies 10 outputtiming 100 binaryoutput no molecular system coordinates output bpti pdb output outputname output bpti dcdfreq 1000 protocol temperature 0 reassignFreq 1000 reassignTemp 25 reassigniIncr 25 reassignHold 300 script minimize 1000 run 20000 32 4 3 Building solvent around a protein The following script illustrates how psfgen and VMD can be used together to add water around a protein structure It assumes you already have a psf and pdb file for your protein as well as a box of water which is large enough to contain the protein For more informat
62. ay be at the beginning of a line This entire line is a comment 14 Some keywords require several lines of data These are generally implemented to either allow the data to be read from a file keyword filename or to be included inline using Tcl style braces keyword lots of data The specification of the keywords is case insensitive so that any combination of upper and lower case letters will have the same meaning Hence DCDfile and dcdfile are equivalent The capitalization in the values however may be important Some values indicate file names in which capitalization is critical Other values such as on or off are case insensitive 2 2 2 Tcl scripting interface and features When compiled with Tcl all released binaries the config file is parsed by Tcl in a fully backwards compatible manner with the added bonus that any Tcl command may also be used This alone allows e the source command to include other files works w o Tcl too e the print command to display messages puts is broken sorry e environment variables through the env array Senv USER and e user defined variables set base sim23 dcdfile base dcd Additional features include e The callback command takes a 2 parameter Tcl procedure which is then called with a list of labels and a list of values during every timestep allowing analysis formatting whatever e The run command takes a number of s
63. binaryoutput lt use binary output files gt Acceptable Values yes or no Default Value yes Description Activates the use of binary output files If this option is set to yes then the final output files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaranteed to be transportable between computer architectures The utility program flipbinpdb is provided with the Linux Intel version to reformat these files e restartname lt restart files gt Acceptable Values UNIX filename prefix Description The prefix to use for restart filenames NAMD produces PDB restart files 20 that store the current positions and velocities of all atoms at some step of the simulation This option specifies the prefix to use for restart files in the same way that outputname specifies a filename prefix for the final positions and velocities If restartname is defined then the parameter restartfreq must also be defined restartfreq lt frequency of restart file generation gt Acceptable Values positive integer Description The number of timesteps between the generation of restart files If restartfreq is defined then restartname must also be defined restartsave lt use timestep in restart filenames gt Acceptable Values yes or no Default Value no Description Appends the current timestep to the restart filename prefix producing a seque
64. bonded evaluation gt Acceptable Values positive integer factor of fullElectFrequency Default Value 1 Description This parameter specifies how often short range nonbonded interactions should be calculated Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where for example one could evaluate bonded forces every 1 fs short range nonbonded forces every 2 fs and long range electrostatics every 4 fs e MTSAlgorithm lt MTS algorithm to be used gt Acceptable Values impulse verletI or constant naive Default Value impulse Description Specifies the multiple timestep algorithm used to integrate the long and short range forces impulse verletI is the same as r RESPA constant naive is the stale force extrapolation method e longSplitting lt how should long and short range forces be split gt Acceptable Values xplor c1 Default Value c1 Description Specifies the method used to split electrostatic forces between long and short range potentials The xplor option uses the X PLOR shifting function and the c1 splitting uses the following C1 continuous shifting function 10 SW rij 0 if Fizl gt Roff SW rij 1 if 5 lt Ron if Roff gt Fizl gt Ron where Ron is a constant defined using the configuration value switchdist Royf is specified using the configuration value cutoff ol e molly lt use mollified impulse method MOLLY gt Acceptable Values on or off Default Value off Des
65. by Phys 4500 Computational Biological Physics Winter 2006 NAMD User s Guide Version 2 5 M Bhandarkar R Brunner C Chipot A Dalke S Dixit P Grayson J Gullingsrud A Gursoy D Hardy W Humphrey D Hurwitz N Krawetz M Nelson J Phillips A Shinozaki G Zheng F Zhu September 29 2003 Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N Mathews Urbana IL 61801 Description The NAMD User s Guide describes how to run and use the various features of the molecular dynamics program NAMD This guide includes the capabilities of the program how to use these capabilities the necessary input files and formats and how to run the program both on uniprocessor machines and in parallel NAMD Version 2 5 Authors M Bhandarkar R Brunner C Chipot A Dalke S Dixit P Grayson J Gullingsrud A Gursoy D Hardy W Humphrey D Hurwitz N Krawetz M Nelson J Phillips A Shinozaki G Zheng F Zhu Theoretical Biophysics Group Beckman Institute University of Illinois 1995 2002 The Board of Trustees of the University of Illinois All Rights Reserved NAMD Molecular Dynamics Software Non Exclusive Non Commercial Use License Introduction The University of Illinois at Urbana Champaign has created its molecular dynamics software NAMD developed by the Theoretical Biophysics Group TBG at Illinois Beckman Institute available free of charge for non
66. ce an interaction electrostatics van der Waals and covalent potential that is divided by the number of copies present In this way the enhanced atoms can occupy the same space while the multiple instances and reduces barriers increase transition rates 6 9 1 Structure Generation To use LES the structure and coordinate input files must be modified to contain multiple copies of the enhanced atoms psfgen provides the multiply command for this purpose NAMD supports a maximum of 15 copies which should be sufficient Begin by generating the complete molecular structure and guessing coordinates as described in Sec 4 As the last operation in your script prior to writing the psf and pdb files add the multiply command specifying the number of copies desired and listing segments residues or atoms to be multiplied For example multiply 4 BPTI 56 BPTI 57 will create four copies of the last two residues of segment BPTI You must include all atoms to be enhanced in a single multiply command in order for the bonded terms in the psf file to be duplicated correctly Calling multiply on connected sets of atoms multiple times will produce unpredictable results as may running other commands after multiply The enhanced atoms are duplicated exactly in the structure they have the same segment residue and atom names They are distinguished only by the value of the B beta column in the pdb file which is 0 for normal atoms and varies from 1 to the number
67. cifications urestraint n restraint or bound specification see below Restraint Specifications not coupled to pmf calculations posi ATOM kf KF ref X Y Z dist 2x ATOM kf KF ref D angle 3x ATOM kf KF ref A dihe 4xATOM barr B ref A Bound Specifications not coupled to pmf calculations posi bound ATOM kf KF low X Y ZD or hi X Y Z D dist bund 2x ATOM kf KF low D or hi D angle bound 3x ATOM kf KF low A or hi A dihe bound 4x ATOM gap E low A0 hi Al delta A2 Forcing Restraint Specifications coupled to pmf calculations posipmf ATOM kf KF low X0 YO Z0 hi X1 Y1 Z1 dist pmf 2x ATOM kf KF low D0 hi D1 angle pmf 3x ATOM kf KF low A0 hi Al dihe pmf 4x ATOM barr B low A0 hi Al Units TT Input item Units E B kcal mol X Y Z D A degrees Ky kcal mol or kcal mol rad 6 7 4 Options for ATOM Specification The designation ATOM above stands for one of the following forms A single atom segname resnum atomname Example insulin 10 ca All atoms of a single residue segname resnum Example insulin 10 A list of atoms group segname resnum atomname segname resnum atomname Example group insulin 10 ca insulin 10 cb insulin 11 cg All atoms in a list of residues group segname resnum segname resnum Example group insulin 10 insulin 12 insulin 14 All atoms in a range of residues group
68. command rescales velocities by the given factor e The measure command allows user programmed calculations to be executed in order to facilitate automated methods For example to revert or change a parameter A number of measure commands are included in the NAMD binary the module has been designed to make it easy for users to add additional measure commands e The coorfile command allows NAMD to perform force and energy analysis on trajectory files coorfile open dcd filename opens the specified DCD file for reading coorfile read reads the next frame in the opened DCD file replacing NAMD s atom coordinates with the coordinates in the frame and returns O if successful or 1 if end of file was reached coorfile skip skips past one frame in the DCD file this is significantly faster than reading coordinates and throwing them away coorfile close closes the file The coorfile command is not available on the Cray T3E Force and energy analysis are especially useful in the context of pair interaction calculations see Sec 6 10 for details as well as the example scripts in Sec 8 Please note that while NAMD has traditionally allowed comments to be started by a appear ing anywhere on a line Tcl only allows comments to appear where a new statement could begin With Tcl config file parsing enabled all shipped binaries both NAMD and Tcl comments are allowed before the first run command At this po
69. cription This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms allowing a fullElectFrequency of 6 vs 4 with a 1 fs timestep without using rigidBonds all You may use rigidBonds water but using rigidBonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen e mollyTolerance lt allowable error for MOLLY gt Acceptable Values positive decimal Default Value 0 00001 Description Convergence criterion for MOLLY algorithm e mollyIterations lt maximum MOLLY iterations gt Acceptable Values positive integer Default Value 100 Description Maximum number of iterations for MOLLY algorithm 52 6 Additional Simulation Parameters 6 1 Constraints and Restraints 6 1 1 Harmonic constraint parameters The following describes the parameters for the harmonic constraints feature of NAMD Actually this feature should be referred to as harmonic restraints rather than constraints but for historical reasons the terminology of harmonic constraints has been carried over from X PLOR This feature allows a harmonic restraining force to be applied to any set of atoms in the simulation e constraints lt are constraints active gt Acceptable Values on or off Default Value off Description Specifies whether or not harmonic constraints are active If it is set to off then no harmonic constraints are comput
70. ct top segid QQQ and x lt xmin or y lt ymin or z lt zmin or x gt xmax or y gt ymax or z gt xmax set overlap atomselect top segid QQQ and within 2 4 of not segid QQQ Get a list of all the residues that are in the two selections and delete those residues from the structure set reslist concat outsidebox get resid overlap get resid set reslist lsort unique integer reslist foreach resid reslist delatom QQQ resid That should do it write out the new psf and pdb file writepsf solvate psf writepdb solvate pdb Delete the combined water protein molecule and load the system that has excess water removed mol delete top mol load psf solvate psf pdb solvate pdb Return the size of the water box return list list xmin ymin zmin list xmax ymax zmax 4 4 List of Commands e topology lt file name gt Purpose Read in molecular topology definitions from file Arguments lt file name gt CHARMM format topology file Context Beginning of script before segment May call multiple times e pdbalias residue lt alternate name gt lt real name gt Purpose Provide translations from residues found in PDB files to proper residue names read in from topology definition files Proper names from topology files will be used in generated PSF and PDB files This command also exists under the deprecated name alias Arguments lt alternate name gt Residue name found i
71. decimal gt 1 0 Default Value 1 0 Description Dielectric constant for the system A value of 1 0 implies no modification of the electrostatic interactions Any larger value will lessen the electrostatic forces acting in the system e 1 4scaling lt scaling factor for 1 4 interactions gt Acceptable Values 0 lt decimal lt 1 Default Value 1 0 46 Description Scaling factor for 1 4 interactions This factor is only used when the exclude parameter is set to scaled1 4 In this case this factor is used to modify the electrostatic inter actions between 1 4 atom pairs If the exclude parameter is set to anything but scaled1 4 this parameter has no effect regardless of its value seed lt random number seed gt Acceptable Values positive integer Default Value pseudo random value based on current UNIX clock time Description Number used to seed the random number generator if temperature or langevin is selected This can be used so that consecutive simulations produce the same results If no value is specified NAMD will choose a pseudo random value based on the current UNIX clock time The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations Note that if Langevin dynamics are used in a parallel simulation i e a simulation using more than one processor even using the same seed will not guarantee reproducible results rigidBonds lt controls if
72. dient for position restraint E K5 2 Trefl E Kp 2 2 Tref yi Yep T zi ze V E Ky as H Tref T F yi z Urey i 2 oz Zref E Gradient for stretch restraint E K 2 di dre di x2 x1 y2 91 22 ajo 81 V E Kj di dref V di for atom 2 moving and atom 1 fixed 2 2 2 71 2 V di 1 2 22 21 y2 91 22 21 2 w2 21 2 yo 91 2 22 21 V di x2 21 T y2 y1 J 22 21 E d V E Kj di dres d 20 9 F 2 21 E Gradient for bend restraint E K5 2 0 bref Atoms at positions A B C distances A to B c A to C b B to C 6 cos u cos a c b 2ac V E Ky 0 reg V Gi VO aby Vle for atom A moving atoms B amp C fixed distances b and c change V u b ac V b a 2c 1 2a al 2ac V c V b ea 20 3 ya yc j za 20 E b V e z4 zB ya yB F 24 28 E c for atom B moving atoms A amp C fixed distances a and c change V u 1 2c c 2a7 b 2a7c V a a 2c 1 2a b 2ac V c V a 28 o yB yo j 2B 20 F a V c zB 24 7 yp ya T zB z4 k c for atom C moving atoms A amp B fized distances a and b oe V u b ac V b c 2a 1 2c b 2ac V a V b 20
73. dihe bound insulin 1 insulin 2 insulin 3 insulin 4 gap 20 low 90 hi 120 delta 10 Forcing restraints a forcing restraint will be imposed on the distance between the centers of mass of residues 10 to 15 and residues 30 to 35 low 20 0 hi 10 0 indicates that the reference distance is 20 0at A 0 and 10 0at A 1 urestraint dist pmf group insulin 10 to insulin 15 group insulin 30 to insulin 35 kf 20 low 20 0 hi 10 0 80 1 during the initial 10 ps increase the strength of the forcing restraint to full strength 0 20 kcal mol 2 2 next apply a force to slowly close the distance from 20 to 10 A changes from 0 1 3 accumulate dU dA for another 10 ps stays fixed at 1 4 force the distance back to its initial value of 20 changes from 1 0 pmf task grow time 10 ps print 1 ps pmf task up time 100 ps pmf task stop time 10 ps pmf task down time 100 ps 1 force the distance to close from 20 to 10 in 5 steps A changes from 0 gt 1 0 2 0 4 0 6 0 8 1 0 at each step equilibrate for 10 ps then collect dU dA for another 10 ps ref 18 16 14 12 10 duration 10 10 x 5 100 ps 2 reverse the step above A changes from 1 0 0 8 0 6 0 4 0 2 0 0 meti task stepup equiltime 10 ps accumtime 10 ps numsteps 5 print 1 ps meti task stepdown 6 7 7 Appendix Gra
74. dinates alanin pdb temperature 0 output params outputname tmp alanin analyze binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 Atoms in group 1 have a 1 in the B column group 2 has a 2 pairInteraction on pairInteractionFile pair pdb pairInteractionCol B pairInteractionGroupi 1 pairInteractionGroup2 2 First frame saved was frame 1000 set ts 1000 coorfile open dcd tmp alanin dcd Read all frames until nonzero is returned while coorfile read 4 Set firstTimestep so our energy output has the correct TS firstTimestep ts Compute energies and forces but don t try to move the atoms run 0 98 incr ts 1000 coorfile close 99 9 Running NAMD NAMD runs on a variety of serial and parallel platforms While it is trivial to launch a serial program a parallel program depends on a platform specific library such as MPI to launch copies of itself on other nodes and to provide access to a high performance network such as Myrinet if one is available For typical workstations Windows Linux Mac OS X or other Unix with only ethernet net working 100 Megabit or Gigabit NAMD uses the Charm native communications layer and the program charmrun to launch namd2 processes for parallel runs either exclusively on t
75. e absolute value e SMDDir lt Direction of the SMD center of mass movement gt Acceptable Values non zero vector Description The direction of the SMD reference position movement The vector does not have to be normalized it is normalized by NAMD before being used e SMDOutputFreq lt frequency of SMD output gt Acceptable Values positive integer Default Value 1 Description The frequency in timesteps with which the current SMD data values are printed out 6 6 6 Interactive Molecular Dynamics IMD NAMD now works directly with VMD to allow you to view and interactively steer your simulation With IMD enabled you can connect to NAMD at any time during the simulation to view the current state of the system or perform interactive steering e IMDon lt is IMD active gt Acceptable Values on or off Default Value off Description Specifies whether or not to listen for an IMD connection e IMDport lt port number to expect a connection on gt Acceptable Values positive integer Description This is a free port number on the machine that node 0 is running on This number will have to be entered into VMD 70 e IMDfreq lt timesteps between sending coordinates gt Acceptable Values positive integer Description This allows coordinates to be sent less often which may increase NAMD performance or be necessary due to a slow network e IMDwait lt wait for an IMD connection gt Acceptable Values yes or no Default Value
76. e capable of generating the required files 2 2 NAMD configuration file Besides these input and output files NAMD also uses a file referred to as the configuration file This file specifies what dynamics options and values that NAMD should use such as the number of timesteps to perform initial temperature etc The options and values in this file control how the system will be simulated A NAMD configuration file contains a set of options and values The options and values specified determine the exact behavior of NAMD what features are active or inactive how long the simulation should continue etc Section 2 2 1 describes how options are specified within a NAMD configuration file Section 2 2 3 lists the parameters which are required to run a basic simulation Section 7 describes the relation between specific NAMD and X PLOR dynamics options Several sample NAMD configuration files are shown in section 8 2 2 1 Configuration parameter syntax Each line in the configuration files consists of a keyword identifying the option being specified and a value which is a parameter to be used for this option The keyword and value can be separated by only white space keyword value or the keyword and value can be separated by an equal sign and white space keyword value Blank lines in the configuration file are ignored Comments are prefaced by a and may appear on the end of a line with actual values keyword value This is a comment or m
77. e enabled then use the non iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm 47 5 3 4 DPMTA parameters DPMTA is no longer included in the released NAMD binaries We recommend that you instead use PME with a periodic system because it conserves energy better is more efficient and is better parallelized If you must have the fast multipole algorithm you may compile NAMD yourself These parameters control the options to DPMTA an algorithm used to provide full electrostatic interactions DPMTA is a modified version of the FMA Fast Multipole Algorithm and unfortu nately most of the parameters still refer to FMA rather than DPMTA for historical reasons Don t be confused For a further description of how exactly full electrostatics are incorporated into NAMD see Section 5 2 For a greater level of detail about DPMTA and the specific meaning of its options see the DPMTA distribution which is available via anonymous FTP from the site ftp ee duke edu in the directory pub SciComp src e FMA lt use full electrostatics gt Acceptable Values on or off Default Value off Description Specifies whether or not the DPMTA algorithm from Duke University should be used to compute the full electrostatic interactions If set to on DPMTA will be used with a multiple timestep integration scheme to provide full electrostatic interactions as detailed in Section 5 2 DPMTA is no longer included in released binaries
78. e is multiplied May be repeated as many times as necessary to include all atoms Context After one or more segments have been built all patches applied and coordinates guessed The effects of this command may confuse other commands delatom lt segid gt resid atom name Purpose Delete one or more atoms If only segid is specified all atoms from that segment will be removed from the structure If both segid and resid are specified all atoms from just that residue will be removed If segid resid and atom name are all specified just a single atom will be removed Arguments lt segid gt Name of segment lt resid gt Name of residue optional lt atom name gt Name of atom optional Context After all segments have been built and patched resetpsf Purpose Delete all segments in from the structure The topology definitions and aliases are left intact Arguments Context After one or more segments have been built psfcontext context new delete Purpose Switches between complete contexts including structure topology definitions and aliases If no arguments are provided the current context is returned If lt context gt or new is specified a new context is entered and the old context is returned If delete is also specified the old context is destroyed and deleted lt old context gt is returned An error is returned if the specified context does not exist or if delete was specified and the specified c
79. e portable to any parallel platform with a modern C compiler to which Charm and Converse have been ported Precompiled NAMD 2 5 binaries are available for the following platforms e Windows NT etc on Intel processors e Mac OS X also called Darwin on PowerPC processors e AIX on RS 6000 processors e HP UX on PA RISC processors e Linux on Intel and Alpha processors e Scyld Beowulf on Intel processors e Clustermatic 3 on Intel processors e Solaris on Sparc processors with and without MPI e Tru64 Unix on Alpha processors with and without MPI e Cray T3E IBM RS 6000 SP using MPI e Compaq AlphaServer SC using the Quadrics Elan library e SGI Origin 2000 with and without MPI 10 3 Compiling NAMD We provide complete and optimized binaries for all platforms to which NAMD has been ported It should not be necessary for you to compile NAMD unless you wish to add or modify features or to improve performance by using an MPI library that takes advantage of special networking hardware Directions for compiling NAMD are contained in the release notes which are available from the NAMD web site http www ks uiuc edu Research namd and are included in all distributions 106 10 4 Documentation All available NAMD documentation is available for download without registration via the NAMD web site http www ks uiuc edu Research namd 107 References 1 10 11 12 13 14 15 M P All
80. ed If it is set to on then harmonic constraints are calculated using the values specified by the parameters consref conskfile conskcol and consexp e consexp lt exponent for harmonic constraint energy function gt Acceptable Values positive even integer Default Value 2 Description Exponent to be use in the harmonic constraint energy function This value must be a positive integer and only even values really make sense This parameter is used only if constraints is set to on e consref lt PDB file containing constraint reference positions gt Acceptable Values UNIX file name Default Value coordinates Description PDB file to use for reference positions for harmonic constraints Each atom that has an active constraint will be constrained about the position specified in this file If no value is given and constraints are active then the same PDB file specified by coordinates will be used instead constraining atoms about their initial positions e conskfile lt PDB file containing force constant values gt Acceptable Values UNIX filename Default Value coordinates Description PDB file to use for force constants for harmonic constraints If this parameter is not specified then the PDB file containing initial coordinates specified by coordinates is used e conskcol lt column of PDB file containing force constant gt Acceptable Values X Y Z 0 or B Default Value 0 Description Column of the PDB file to use for the har
81. efault NAMD applies switching functions to the non bond interactions within the cut off distance which helps to improve energy conservation while AMBER does not use switching functions so it simply truncates the interactions at cutoff However if authentic AMBER cutoff simulations are desired the switching functions could be turned off by specifying switching off in NAMD configuration file 6 When SHAKE is applied to water molecules NAMD constrains the two O H bonds and the H O H angle which produces the same result as constraining the additional H H bond But in some AMBER models water is defined by three real bonds and no angle In this case NAMD will apply SHAKE only to the two O H bonds and not to the angle or the H H bond because the angle is not defined Thus when SHAKE is used along with this kind of water model difference would be expected between NAMD and AMBER 7 NAMD and AMBER may have different default values for some parameters e g the tolerance of SHAKE One should check other sections of this manual for accurate descriptions of the NAMD options Following are two examples of the NAMD configuration file to read AMBER force field and carry out simulation They may help users to select proper NAMD options for AMBER force field For the convenience of AMBER users the AMBER 6 sander input files are given in the left for comparison which would accomplish similar tasks in AMBER Example 1 Non periodic boundary
82. electrostatics directly gt Acceptable Values yes or no Default Value no Description Specifies whether or not direct computation of full electrostatics should be performed 50 5 3 7 Multiple timestep parameters One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple timestep integration Currently the only available method is the impulse based Verlet I or r RESPA method which is stable for timesteps up to 4 fs for long range electrostatic forces 2 fs for short range nonbonded forces and 1 fs for bonded forces Setting rigid all i e using SHAKE increases these timesteps to 6 fs 2 fs and 2 fs respectively but eliminates bond motion for hydrogen The mollified impulse method MOLLY reduces the resonance which limits the timesteps and thus increases these timesteps to 6 fs 2 fs and 1 fs while retaining all bond motion e fullElectFrequency lt number of timesteps between full electrostatic evaluations gt Acceptable Values positive integer factor of stepspercycle Default Value nonbondedFreq Description This parameter specifies the number of timesteps between each full elec trostatics evaluation It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed 4 0 unless rigidBonds all or molly on is specified in which case the upper limit is perhaps doubled e nonbondedFreg lt timesteps between non
83. en and D J Tildesley Computer Simulation of Liquids Oxford University Press New York 1987 P H Axelsen and D Li Improved convergence in dual topology free energy calculations through use of harmonic restraints J Comput Chem 19 1278 1283 1998 F C Bernstein T F Koetzle G J B Williams J E F Meyer M D Brice J R Rodgers O Kennard T Shimanouchi and M Tasumi The protein data bank A computer based archival file for macromolecular structures J Mol Biol 112 535 542 1977 D L Beveridge and F M DiCapua Free energy via molecular simulation applications to chemical and biomolecualr systems Ann Rev Biophys Biophys Chem 18 431 492 1989 S Boresch and M Karplus The role of bonded terms in free energy simulations 1 theoretical analysis J Phys Chem A 103 103 118 1999 B R Brooks R E Bruccoleri B D Olafson D J States S Swaminathan and M Karplus CHARMM a program for macromolecular energy minimization and dynamics calculations J Comp Chem 4 2 187 217 1983 A T Br nger X PLOR Version 3 1 A System for X ray Crystallography and NMR The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry Yale University 1992 C Chipot and D A Pearlman Free energy calculations the long and winding gilded road Mol Sim 2001 M K Gilson J A Given B L Bush and J A McCammon The statistical thermodynamic basis for computation
84. er Eo and two reference angles xo and x1 E Eo 2 1 cos xi Xref Xref AX1 1 A xo The forcing restraints depend on the coupling parameter A specified in a conformational forcing calculation For example the restraint distance d ef depends on A and as changes two atoms or centers of mass are forced closer together or further apart In this case Ky Kyo the value supplied at input Alternatively the value of kK may depend upon the coupling parameter according to Ky Kfo Bounds Position bound 1 atom Force constant K reference position Tref and upper or lower reference distance dref Upper bound E Ky 2 di dre for di gt dref else E 0 Lower bound E Ky 2 di dref for di lt dref else E 0 79 Pay Distance bound 2 atoms Force constant Kp and upper or lower reference distance dref Upper bound E K 2 dij dref for dij gt dref else E 0 Lower bound E K 2 dij dref for dij lt dref else E 0 Angle bound 3 atoms Force constant Ky and upper or lower reference angle Oref Upper bound E Ky 2 0 bref for 0 gt Ores else E 0 Lower bound E K5 2 0 Ores for 0 lt Ores else E 0 Torsion bound 4 atoms An upper and lower bound must be provided together Energy gap Eo lower AND upper reference angles x and x2 and angle interval Ax X1 lt X lt X2 E 0 Pa Ay lt x E E G 2 1 cos x
85. eraging over pressure measure ments and hence smaller fluctuations in the cell volume A reasonable choice for relaxation time would be 100 fs The compressibility and the relaxation time appear only as a ratio in the dynamics so a larger compressibility is equivalent to a smaller relaxation time BerendsenPressureFreq lt how often to rescale positions gt Acceptable Values positive multiple of nonbondedFrequency and fullElectFrequency Default Value nonbondedFrequency or fullElectFrequency if used Description Specifies number of timesteps between position rescalings for Berendsen s method Primarily to deal with multiple timestepping integrators but also to reduce cell volume fluctuations cell rescalings can occur on a longer interval This could reasonably be between 1 and 20 timesteps but the relaxation time should be at least ten times larger 6 5 2 Nos Hoover Langevin piston pressure control NAMD provides constant pressure simulation using a modified Nos Hoover method in which Langevin dynamics is used to control fluctuations in the barostat This method should be combined with a method of temperature control such as Langevin dynamics in order to simulate the NPT ensemble The Langevin piston Nose Hoover method in NAMD is a combination of the Nose Hoover constant pressure method as described in GJ Martyna DJ Tobias and ML Klein Constant pressure molecular dynamics algorithms J Chem Phys 101 5 1994 with piston fl
86. ergy calculation is biotinr fepout in which energies are written every 5 steps 6A the width of the windows is set to 0 1 5000 MD steps are performed in each window to equilibrate the system In this particular instance the current value of A is controlled by the statement set step The FEP calculation is run until A reaches the value 0 9 In every window 10000 MD steps are performed 87 6 8 4 Description of FEP simulation output The fepOutFile contains electrostatic and van der Waals energy data calculated at A and A2 writ ten every fepOutFreq steps The column dE is the instantaneous energy difference for the current configuration dE_avg and dG are the accumulated energy ensemble average and the corresponding free energy at the current time step respectively The temperature is specified in the penultimate column Upon completion of fepEquilSteps steps the calculation of dE_avg and dG is restarted The accumulated net free energy change is output at each A value and at the end of the simulation The cumulative average energy dE_avg value may be summed using for instance the trapezoidal rule or a Gaussian quadrature to obtain an approximate TI estimate for the free energy change during the run 6 9 Locally Enhanced Sampling Locally enhanced sampling LES 16 17 18 increases sampling and transition rates for a portion of a molecule by the use of multiple non interacting copies of the enhanced atoms These enhanced atoms experien
87. ers lt parameter file gt Acceptable Values UNIX filename Description A CHARMM19 or CHARMM22 parameter file that defines all or part of the parameters necessary for the molecular system to be simulated At least one parameter file must be specified for each simulation Multiple definitions but only one file per definition are allowed for systems that require more than one parameter file The files will be read in the order that they appear in the configuration file If duplicate parameters are read a warning message is printed and the last parameter value read is used Thus the order that files are read can be important in cases where duplicate values appear in separate files paraTypeXplor lt Is the parameter file in X PLOR format gt Acceptable Values on or off Default Value on Description Specifies whether or not the parameter file s are in X PLOR format X PLOR format is the default for parameter files Caveat The PSF file should be also con structed with X PLOR in case of an X PLOR parameter file because X PLOR stores in formation about the multiplicity of dihedrals in the PSF file See the X PLOR manual for details paraTypeCharmm lt Is the parameter file in CHARMM format gt Acceptable Values on or off Default Value off Description Specifies whether or not the parameter file s are in CHARMM format X PLOR format is the default for parameter files Caveat The information about multiplicity of dihedrals wil
88. ery time an atom exceeds a trigger criterion that is some fraction of the tolerance distance the tolerance is increased by this fraction pairlistTrigger lt trigger is atom beyond 1 x tol gt Acceptable Values non negative decimal Default Value 0 3 Description The goal of pairlist tolerance adjustment is to make pairlist invalidations rare while keeping the tolerance as small as possible for best performance Rather than monitoring the very rare case where atoms actually move more than the tolerance distance 45 we reduce the trigger tolerance by this fraction The tolerance is increased whenever the trigger tolerance is exceeded as specified by pairlistGrow 5 3 3 Basic dynamics e exclude lt exclusion policy to use gt Acceptable Values none 1 2 1 3 1 4 or scaled1 4 Description This parameter specifies which pairs of bonded atoms should be excluded from non bonded interactions With the value of none no bonded pairs of atoms will be excluded With the value of 1 2 all atom pairs that are directly connected via a linear bond will be excluded With the value of 1 3 all 1 2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom i e if atom A is bonded to atom B and atom B is bonded to atom C then the atom pair A C would be excluded With the value of 1 4 all 1 3 pairs will be excluded along with all pairs connected by a set of two bonds e if atom A is bonded to atom
89. erything until ENDMOL as input You may run psfgen interactively as well Since psfgen is built on a Tcl interpreter you may use loops variables etc but you must use for variables when inside a shell script If you want run psfgen and enter the following commands manually 30 3 Read topology file Read in the topology definitions for the residues we will create This must match the parameter file used for the simulation as well Multiple topology files may be read in since psfgen and NAMD use atom type names rather than numbers in psf files 4 Build protein segment Actually build a segment calling it BPTI and reading the sequence of residues from the stripped pdb file created above In addition to the pdb command we could specify residues explicitly Both angles and dihedrals are generated automatically unless auto none is added which is required to build residues of water The commands first and last may be used to change the default patches for the ends of the chain The structure is built when the closing is encountered and some errors regarding the first and last residue are normal 5 Patch protein segment Some patch residues those not used to begin or end a chain are applied after the segment is built These contain all angle and dihedral terms explicitly since they were already generated In this case we apply the patch for a disulfide link three separate times 6 Read protein coordinates fro
90. esteps i e the r RESPA integrator is used For appropriate values of k it is believed that the error introduced by this infrequent evaluation is modest compared to the error already incurred by the use of the numerical Verlet integrator Improved methods for incorporating these long range forces are currently being investigated with the intention of improving accuracy as well as reducing the frequency of long range force evaluations In the scheme described above the van der Waals forces are still truncated at the local interac tion distance Thus the van der Waals cutoff distance forms a lower limit to the local interaction distance While this is believed to be sufficient there are investigations underway to remove this limitation and provide full van der Waals calculations in O N time as well 5 3 NAMD configuration parameters 5 3 1 Timestep parameters e numsteps lt number of timesteps gt Acceptable Values positive integer Description The number of simulation timesteps to be performed An integer greater than 0 is acceptable The total amount of simulation time is numsteps x timestep e timestep lt timestep size fs gt Acceptable Values non negative decimal Default Value 1 0 Description The timestep size to use when integrating each step of the simulation The value is specified in femtoseconds e firsttimestep lt starting timestep value gt Acceptable Values non negative integer Default Value 0 Description
91. evelopers of the code e FMAFFTBlock lt blocking factor for FMA FFT gt Acceptable Values positive integer Default Value 4 Description The blocking factor for the FFT enhancement to DPMTA This parameter is only used if both FMA and FMAFFT are set to on The default value of 4 should be suitable for most applications 5 3 5 PME parameters PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions None of the parameters should affect energy conservation although they may affect the accuracy of the results and momentum conservation e PME lt Use particle mesh Ewald for electrostatics gt Acceptable Values yes or no Default Value no Description Turns on particle mesh Ewald e PMETolerance lt PME direct space tolerance gt Acceptable Values positive decimal Default Value 107 Description Affects the value of the Ewald coefficient and the overall accuracy of the results e PMEInterpOrder lt PME interpolation order gt Acceptable Values positive integer Default Value 4 cubic Description Charges are interpolated onto the grid and forces are interpolated off using this many points equal to the order of the interpolation function plus one e PMEGridSizeX lt number of grid points in x dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeX should
92. file When gromacs is set to on either grocoorfile or coordinates must be defined but not both However NAMD does not have support for many GROMACS specific options e Dummies fake atoms with positions generated from the positions of real atoms are not supported e The GROMACS pairs section where explicit 1 4 parameters are given between pairs of atoms is not supported since NAMD calculates its 1 4 interactions exclusively by type e Similarly exclusions are not supported The biggest problem here is that GROMACS RB dihedrals are supposed to imply exclusions but NAMD does not support this e Constraints restraints and settles are not implemented in NAMD e In some cases it may not work to override some but not all of the parameters for a bond atom etc In this case NAMD will generate an error and stop The parser will sometimes not tolerate correct GROMACS files or fail to detect errors in badly formatted files e NAMD does not support all the types of bond potentials that exist in GROMACS but approximates them with harmonic or sinusoidal potentials e NAMD does not read periodic box lengths in the coordinate file They must be explicitly specified in the NAMD configuration file 26 4 Creating PSF Structure Files The psfgen structure building tool consists of a portable library of structure and file manipulation routines with a Tcl interface Current capabilities include e reading CHARMM topology files e reading
93. fileNonbonded lt Compute nonbonded pressure profile contribution gt Acceptable Values on or off Default Value off Description When enabled only the nonbonded contribution to the pressure profile will be computed For trajectory analysis the recommended way to use this option is to use the NAMD Tel scripting interface as described in Sec 2 2 2 to run for 0 steps so that NAMD prints the pressure profile without performing any dynamics Here is an example snippet from a NAMD input that can be used to compute the nonbonded component of the pressure profile It assumes that the coordinates were saved in three dcd files pp01 dcd pp02 dcd and pp03 dcd every 500 timesteps The pressureProfileSlabs must be the same as was used for the calculation of the bonded part of the pressure Note the use of no switching function this way the calculated electrostatic energy will be closest to what would be calculated by PME switching off cutoff 20 0 pairlistdist 20 5 pressureProfile on pressureProfileSlabs 60 pressureProfileFreq 100 pressureProfileNonbonded on 91 Assume that coordinates were written to the dcd files every 500 timesteps set ts 500 foreach dcd pp01 dcd pp02 dcd pp03 dcd coorfile open dcd dcd while 4 coorfile read 1 firstTimestep ts run O incr ts 500 coorfile close 92 7 Translation between NAMD and X PLOR configuration param eters NAMD was designed to provide many of the same molecular dyn
94. g Parallel Scaling While NAMD is designed to be a scalable program particularly for simulations of 100 000 atoms or more at some point adding additional processors to a simulation will provide little or no extra performance If you are lucky enough to have access to a parallel machine you should measure NAMD s parallel speedup for a variety of processor counts when running your particular simulation The easiest and most accurate way to do this is to look at the Benchmark time lines that are printed after 20 and 25 cycles usually less than 500 steps You can monitor performance during the entire simulation by adding outputTiming steps to your configuration file but be careful to look at the wall time rather than CPU time fields on the TIMING output lines produced For an external measure of performance you should run simulations of both 25 and 50 cycles see the stepspercycle parameter and base your estimate on the additional time needed for the longer simulation in order to exclude startup costs and allow for initial load balancing We provide both standard UDP and new TCP based precompiled binaries for Linux clusters We have observed that the TCP version is better on our dual processor clusters with gigabit ethernet while the basic UDP version is superior on our single processor fast ethernet cluster When using the UDP version with gigabit you can add the giga option to adjust several tuning parameters Additi
95. gged as constrained The PDB file also gives initial coordinates for the constraint positions One also specifies such parameters as the force constant s for the constraints and the velocity with which the constraints move There are two major differences between SMD and harmonic constraints e In harmonic constraints each tagged atom is harmonically constrained to a reference point which moves with constant velocity In SMD it is the center of mass of the tagged atoms which is constrained to move with constant velocity e In harmonic constraints each tagged atom is constrained in all three spatial dimensions In SMD tagged atoms are constrained only along the constraint direction The center of mass of the SMD atoms will be harmonically constrained with force constant k SMDk to move with velocity v SMDVel in the direction 7 SMDDir SMD thus results in the following potential being applied to the system k vt A t Ro al 2 Dl at 5 Here t Nisdt where Nts is the number of elapsed timesteps in the simulation and dt is the size of the timestep in femtoseconds Also R t is the current center of mass of the SMD atoms and Ro is the initial center of mass as defined by the coordinates in SMDFile Vector is normalized by NAMD before being used Output NAMD provides output of the current SMD data The frequency of output is specified by the SMDOutputFreq parameter in the configuration file Every SMDOutputFreq t
96. gin providing hexagonal or other cell shapes 6 5 Pressure Control Constant pressure simulation and pressure calculation require periodic boundary conditions Pres sure is controlled by dynamically adjusting the size of the unit cell and rescaling all atomic coordi nates other than those of fixed atoms during the simulation Pressure values in NAMD output are in bar PRESSURE is the pressure calculated based on individual atoms while GPRESSURE incorporates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluctuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE The phenomenological pressure of bulk matter reflects averaging in both space and time of the sum of a large positive term the kinetic pressure nRT V and a large cancelling negative term the static pressure The instantaneous pressure of a simulation cell as simulated by NAMD will have mean square fluctuations according to David Case quoting Section 114 of Statistical Physics by Landau and Lifshitz of kT V 6 where 8 is the compressibility which is RMS of roughly 100 bar for a 10 000 atom biomolecular system Much larger fluctuations are regularly observed in practice The instantaneous pressure for a biomolecular system is well defined for internal forces that are ba
97. have only small integer factors 2 3 and 5 e PMEGridSizeY lt number of grid points in y dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeY should have only small integer factors 2 3 and 5 e PMEGridSizeZ lt number of grid points in z dimension gt Acceptable Values positive integer Description The grid size partially determines the accuracy and efficiency of PME For speed PMEGridSizeZ should have only small integer factors 2 3 and 5 e PMEProcessors lt processors for FFT and reciprocal sum gt Acceptable Values positive integer 49 Default Value larger of x and y grid sizes up to all available processors Description For best performance on some systems and machines it may be necessary to restrict the amount of parallelism used Experiment with this parameter if your parallel performance is poor when PME is used FFTWEstimate lt Use estimates to optimize FFT gt Acceptable Values yes or no Default Value no Description Do not optimize FFT based on measurements but on FF TW rules of thumb This reduces startup time but may affect performance FFTWUseWisdom lt Use FF TW wisdom archive file gt Acceptable Values yes or no Default Value yes Description Try to reduce startup time when possible by reading FFTW wisdom from a file and saving wisdom generated by performance measurements to
98. he initial reference position Ro at t 0 R M Ro P P where P is the pivot point Coordinates of point N can be found as N P R P v v Normal from the atom pos to the axis is similarly normal P X P v v X The force is as usual F K R X This is the force applied to the atom in NAMD see below NAMD does not know anything about the torque applied However the torque applied to the atom can be calculated as a vector product torque F x normal Finally the torque applied to the atom with respect to the axis is the projection of the torque on the axis i e torquepro torque v If there are atoms that have to be constrained but not moved this implementation is not suitable because it will move all reference positions Only one of the moving and rotating constraints can be used at a time Using very soft springs for rotating constraints leads to the system lagging behind the reference positions and then the force is applied along a direction different from the ideal direction along the circular path Pulling on N atoms at the same time with a spring of stiffness K amounts to pulling on the whole system by a spring of stiffness NK so the overall behavior of the system is as if you are pulling with a very stiff spring if N is large In both moving and rotating constraints the force constant that you specify in the constraints pdb file is multiplied by 2 for the force calculation i e if you spec
99. he local machine with the local option or on other hosts as specified by a nodelist file The namd2 binaries for these platforms can also be run directly known as standalone mode for single process runs For workstation clusters and other massively parallel machines with special high performance networking NAMD uses the system provided MPI library with a few exceptions and standard system tools such as mpirun are used to launch jobs Since MPI libraries are very often incompatible between versions you will likely need to recompile NAMD and its underlying Charm libraries to use these machines in parallel the provided non MPI binaries should still work for serial runs The provided charmrun program for these platforms is only a script that attempts to translate charmrun options into mpirun options but due to the diversity of MPI libraries it often fails to work 9 1 Individual Windows Linux Mac OS X or Other Unix Workstations Individual workstations use the same version of NAMD as workstation networks but running NAMD is much easier If your machine has only one processor you can run the namd2 binary directly namd2 lt configfile gt For multiprocessor workstations Windows and Solaris released binaries are based on SMP versions of Charm that can run multiple threads For best performance use one thread per processor with the p option namd2 p lt procs gt lt configfile gt Since the SMP versions of NAMD are relatively ne
100. ial period T1 then dU dA is accumulated for T2 Therefore the total duration of an mcti block is T1 T2 x N 6 7 6 Examples Fixed restraints 1 restrain the position of the ca atom of residue 0 2 restrain the distance between the ca s of residues 0 and 10 to 5 2A 3 restrain the angle between the ca s of residues 0 10 20 to 90 4 restrain the dihedral angle between the ca s of residues 0 10 20 30 to 180 5 restrain the angle between the centers of mass of residues 0 10 20 to 90 urestraint posi insulin 0 ca kf 20 ref 10 11 11 dist insulin 0 ca insulin 10 ca kf 20 ref 5 2 79 angle insulin 0 ca insulin 10 ca insulin 20 ca kf 20 ref 90 dihe insulin 0 ca insulin 10 ca insulin 20 ca insulin 30 ca barr 20 ref 180 angle insulin 0 insulin 10 insulin 20 kf 20 ref 90 IFE restrain the center of mass of three atoms of residue 0 2 restrain the distance between the COM of 3 atoms of residue 0 to the COM of 3 atoms of residue 10 3 restrain the dihedral angle of 10 11 12 15 16 17 18 20 22 30 31 32 34 35 to 90 ca of 10 to 12 ca cb cg of 15 to 18 all atoms of 20 and 22 ca of 30 31 32 34 all atoms of 35 urestraint posi group insulin 0 ca insulin 0 cb insulin 0 cg kf 20 ref 10 11 11 dist group insulin 0 ca insulin 0 cb insulin 0 cg group insulin 10 ca insulin 10 cb
101. ified K 0 5 kcal mol A in the pdb file the force actually calculated is F 2kK R X 1 keal mol A R X SMD feature of namd2 does the calculation without multiplication of the force constant specified in the config file by 2 e rotConstraints lt Are rotating constraints active gt Acceptable Values on or off Default Value off Description Should rotating restraints be applied to the system If set to on then rotConsAxis rotConsPivot and rotConsVel must be defined May not be used with movingConstraints 68 e rotConsAxis lt Axis of rotation gt Acceptable Values vector may be unnormalized Description Axis of rotation Can be any vector It gets normalized before use If the vector is 0 no rotation will be performed but the calculations will still be done e rotConsPivot lt Pivot point of rotation gt Acceptable Values position in A Description Pivot point of rotation The rotation axis vector only gives the direction of the axis Pivot point places the axis in space so that the axis goes through the pivot point e rotConsVel lt Angular velocity of rotation gt Acceptable Values rate in degrees per timestep Description Angular velocity of rotation degrees timestep 6 6 5 Steered Molecular Dynamics SMD The SMD feature is independent from the harmonic constraints although it follows the same ideas In both SMD and harmonic constraints one specifies a PDB file which indicates which atoms are ta
102. ifies the distance at which the switching function should start taking effect to bring the van der Waals potential to 0 smoothly at the cutoff distance Thus the value of switchdist must always be less than that of cutoff 5 1 2 Non bonded electrostatic interactions The handling of electrostatics is slightly more complicated due to the incorporation of multiple timestepping for full electrostatic interactions There are two cases to consider one where full electrostatics is employed and the other where electrostatics are truncated at a given distance First let us consider the latter case where electrostatics are truncated at the cutoff distance Using this scheme all electrostatic interactions beyond a specified distance are ignored or assumed to be zero If switching is set to on rather than having a discontinuity in the potential at the 39 cutoff distance a shifting function is applied to the electrostatic potential as shown in Figure 2 As this figure shows the shifting function shifts the entire potential curve so that the curve intersects the x axis at the cutoff distance This shifting function is based on the shifting function used by X PLOR energy E 0 cutoff distance Figure 2 Graph showing an electrostatic potential with and without the application of the shifting function Next consider the case where full electrostatics are calculated In this case the electrostatic interactions are not truncated
103. imesteps NAMD will print the current timestep current position of the center of mass of the restrained atoms and the current force applied to the center of mass in piconewtons pN The output line starts with word SMD 69 Parameters The following parameters describe the parameters for the SMD feature of NAMD e SMD lt Are SMD features active gt Acceptable Values on or off Default Value off Description Should SMD harmonic constraint be applied to the system If set to on then SMDk SMDFile SMDVel and SMDDir must be defined Specifying SMDOutputFreq is optional e SMDFile lt SMD constraint reference position gt Acceptable Values UNIX filename Description File to use for the initial reference position for the SMD harmonic constraints All atoms in this PDB file with a nonzero value in the occupancy column will be tagged as SMD atoms The coordinates of the tagged SMD atoms will be used to calculate the initial center of mass During the simulation this center of mass will move with velocity SMDVel in the direction SMDDir e SMDk lt force constant to use in SMD simulation gt Acceptable Values positive real Description SMD harmonic constraint force constant Must be specified in kcal mol A The conversion factor is 1 kcal mol 69 479 pN A e SMDVel lt Velocity of the SMD reference position movement gt Acceptable Values nonzero real A timestep Description The velocity of the SMD center of mass movement Gives th
104. int only pure Tcl syntax is allowed In addition the idiom for Tcl comments will only work with Tcl enabled NAMD has also traditionally allowed parameters to be specified as param value This is supported but only before the first run command Some examples this is my config file lt OK reassignFreq 100 how often to reset velocities lt only w Tcl reassignTemp 20 temp to reset velocities to lt OK before run run 1000 lt now Tcl only reassignTemp 40 temp to reset velocities to lt is required NAMD has also traditionally allowed parameters to be specified as param value as well as param value This is supported but only before the first run command For an easy life use param value 2 2 3 Required NAMD configuration parameters The following parameters are required for every NAMD simulation e numsteps page 43 e coordinates page 19 e structure page 19 16 e parameters page 19 e exclude page 46 e outputname page 20 e one of the following three temperature page 46 velocities page 19 binvelocities page 20 These required parameters specify the most basic properties of the simulation In addition it is highly recommended that pairlistdist be specified with a value at least one greater than cutoff 17 3 Input and Output Files NAMD was developed to be compatible with existing molecular dynamics packages especi
105. ion on how atomselections can be used within VMD scripts see the VMD User s Guide proc addwater psffile pdbfile watpsf watpdb Create psf pdb files that contain both our protein as well as a box of equilibrated water The water box should be large enough to easily contain our protein resetpsf readpsf psffile readpsf watpsf coordpdb pdbfile coordpdb watpdb Load the combined structure into VMD writepsf combine psf writepdb combine pdb mol load psf combine psf pdb combine pdb Assume that the segid of the water in watpsf is QQQ We want to delete waters outside of a box ten Angstroms bigger than the extent of the protein set protein atomselect top not segid QQQ set minmax measure minmax protein foreach min max minmax break foreach xmin ymin zmin min break foreach xmax ymax zmax max break set xmin expr xmin 10 set ymin expr ymin 10 set zmin expr zmin 10 set xmax expr xmax 10 set ymax expr ymax 10 set zmax expr zmax 10 Center the water on the protein Also update the coordinates held by psfgen set wat atomselect top segid QQQ wat moveby vecsub measure center protein measure center wat foreach atom wat get segid resid name x y z 4 foreach segid resid name x y z atom break coord segid resid name list x y z Select waters that we don t want in the final structure 33 set outsidebox atomsele
106. ion target Must be used with useFlexibleCell and periodic boundary conditions The pressure specified in LangevinPistonTarget becomes the pressure along the z axis and surface tension is applied in the x y plane e StrainRate lt initial strain rate gt Acceptable Values decimal triple x y z Default Value 0 0 0 Description Optionally specifies the initial strain rate for pressure control Is overridden by value read from file specified with extendedSystem There is typically no reason to set this parameter e ExcludeFromPressure lt Should some atoms be excluded from pressure rescaling gt Acceptable Values on or off Default Value off Description Specifies whether or not to exclude some atoms from pressure rescaling The coordinates and velocites of such atoms are not rescaled during constant pressure simulations though they do contribute to the virial calculation May be useful for membrane protein simulation EXPERIMENTAL e ExcludeFromPressureFile lt File specifying excluded atoms gt Acceptable Values PDB file Default Value coordinates file Description PDB file with one column specifying which atoms to exclude from pressure rescaling Specify 1 for excluded and 0 for not excluded e ExcludeFromPressureCol lt Column in PDB file for specifying excluded atoms gt Acceptable Values O B X Y or Z Default Value O Description Specifies which column of the pdb file to check for excluded atoms 6 6 Applied Forces
107. is parameter only has meaning if switching is set to on The value of switchdist must be less than or equal to the value of cutoff since the switching function is only applied on the range from switchdist to cutoff For a complete description of the non bonded force parameters see Section 5 1 e pairlistdist lt distance between pairs for inclusion in pair lists A gt Acceptable Values positive decimal gt cutoff Default Value cutoff Description A pair list is generated pairlistsPerCycle times each cycle containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list This parameter is equivalent to the X PLOR parameter CUTNb If no atom moves more than pairlistdist cutoff during one cycle then there will be no jump in electrostatic or van der Waals energies when the next pair list is built Since such a jump is unavoidable when truncation is used this parameter may only be specified when switching is set to on If this parameter is not specified and switching is set to on the value of cutoff is used A value of at least one greater than cutoff is recommended e splitPatch lt how to assign atoms to patches gt Acceptable Values position or hydrogen Default Value hydrogen Description When set to hydrogen hydrogen atoms are kept on the same patch as their parents al
108. istance As the pair moved closer and entered the cutoff distance because the pair was already in the pair list the non bonded interactions would immediately be calculated and energy conservation would be preserved The value of pairlistdist should be chosen such that no atom pair moves more than pairlistdist cutoff in one cycle This will insure energy conservation and efficiency The pairlistdist parameter is also used to determine the minimum patch size Unless the splitPatch parameter is explicitly set to position hydrogen atoms will be placed on the same patch as the mother atom to which they are bonded These hydrogen groups are then distance tested against each other using only a cutoff increased by the the value of the hgroupCutoff parameter The size of the patches is also increased by this amount NAMD functions correctly even if a hydrogen atom and its mother atom are separated by more than half of hgroupCutoff by breaking that group into its individual atoms for distance testing Margin violation warning messages are printed if an atom moves outside of a safe zone surrounding the patch to which it is assigned indicating that pairlistdist should be increased in order for forces to be calculated correctly and energy to be conserved Margin violations mean that atoms that are in non neighboring patches may be closer than the cutoff distance apart This may sometimes happen in constant pressure simulations when the cell shrinks since
109. it would be possible for atoms to drift closer to gether than the cutoff distance during subsequent timesteps and yet not have their non bonded interactions calculated Let us consider a concrete example to better understand this Assume that the pairlist is built once every ten timesteps and that the cutoff distance is 8 0 A Consider a pair of atoms A and B that are 8 1 A apart when the pairlist is built If the pair list includes only those atoms within the cutoff distance this pair would not be included in the list Now assume that after five timesteps atoms A and B have moved to only 7 9 A apart A and B are now within the cutoff distance of each other and should have their non bonded interactions calculated However because the non bonded interactions are based solely on the pair list and the pair list will not be rebuilt for another five timesteps this pair will be ignored for five timesteps causing energy not to be conserved within the system To avoid this problem the parameter pairlistdist allows the user to specify a distance greater than the cutoff distance for pairs to be included in the pair list as shown in Figure 4 Pairs that are included in the pair list but are outside the cutoff distance are simply ignored So in the above example if the pairlistdist were set to 10 0 A then the atom pair A and B would be included in the pair list even though the pair would initially be ignored because they are further apart than the cutoff d
110. ithm is not the most rapidly convergent it is sufficient for most applications There are only two parameters for minimization one to activate minimization and another to specify the maximum movement of any atom e velocityQuenching lt Perform old style energy minimization gt Acceptable Values on or off Default Value off Description Turns slow energy minimization on or off 55 e maximumMove lt maximum distance an atom can move during each step A gt 6 3 Acceptable Values positive decimal Default Value 0 75 x cutoff stepsPerCycle Description Maximum distance that an atom can move during any single timestep of minimization This is to insure that atoms do not go flying off into space during the first few timesteps when the largest energy conflicts are resolved Temperature Control and Equilibration 6 3 1 Langevin dynamics parameters NAMD is capable of performing Langevin dynamics where additional damping and random forces are introduced to the system This capability is based on that implemented in X PLOR which is detailed in the X PLOR User s Manual 7 although a different integrator is used langevin lt use Langevin dynamics gt Acceptable Values on or off Default Value off Description Specifies whether or not Langevin dynamics active If set to on then the parameter langevinTemp must be set and the parameters langevinFile and langevinCol can optionally be set to control the behavior of this feature
111. ive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 cylindricalBCr2 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect along the non axis plane of the cylinder If this parameter is defined then cylindricalBC12 and spericalBCk2 must also be defined cylindricalBCl2 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect along the cylinder axis If this parameter is defined then cylindricalBCr2 and spericalBCk2 must also be defined cylindricalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center 60 e cylindricalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 6 4 3 Periodic boundary conditions NAMD provides periodic boundary conditions in 1 2 or 3 dimensions The following parameters are used to define these boundary conditions e cellBasisVector1
112. ive integer less than lesFactor The parameter lesFactor may be varied between simulations to interpolate between full en hancement and normal simulation although multiple bonded images are present at all times If lesFactor is decreased the images with flags greater than lesFactor will be decoupled from non bonded terms sample based only on bonded terms and should therefore be excluded from analysis When increasing lesFactor the coordinates of these abandoned images should be reset to that of another image to avoid any bad initial contacts and the resulting instability in the simulation 6 10 Pair Interaction Calculations NAMD supportes the calculation of interaction energy calculations between two groups of atoms When enabled pair interaction information will be calculated and printed in the standard output file on its own line at the same frequency as energy output The format of the line is PAIR INTERACTION STEP step VDW_FORCE fx fy fz ELECT_FORCE fx fy fz The displayed force is the force on atoms in group 1 and is units of kcal mol A For trajectory analysis the recommended way to use this set of options is to use the NAMD Tcl scripting interface as described in Sec 2 2 2 to run for 0 steps so that NAMD prints the energy without performing any dynamics e pairInteraction lt is pair interaction calculation active gt Acceptable Values on or off Default Value off Description Specifies whether pair interaction calculation
113. l be obtained directly from the parameter file and the full multiplicity will be used same behavior as in CHARMM If the PSF file originates from X PLOR consecutive multiple entries for the same dihedral indicating the dihedral multiplicity for X PLOR will be ignored velocities lt velocity PDB file gt Acceptable Values UNIX filename Description The PDB file containing the initial velocities for all atoms in the simulation This is typically a restart file or final velocity file written by NAMD during a previous simu lation Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together 19 e binvelocities lt binary velocity file gt Acceptable Values UNIX filename Description The binary file containing initial velocities for all atoms in the simulation A binary velocity file is created as output from NAMD by activating the binaryrestart or binaryoutput options The binvelocities option should be used as an alternative to velocities Either the temperature or the velocities binvelocities option must be defined to determine an initial set of velocities Both options cannot be used together e bincoordinates lt binary coordinate restart file gt Acceptable Values UNIX filename Description The binary restart file containing initial position coordinate data A binary coordinate restart file is created as output from NAMD by activati
114. liance with any of its terms Licensee may be held legally responsible for any copyright infringement that is caused or encouraged by its failure to abide by the terms of this license Upon termination Licensee agrees to destroy all copies of the Software in its possession and to verify such destruction in writing 6 The user agrees that any reports or published results obtained with the Software will ac knowledge its use by the appropriate citation as follows NAMD was developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana Champaign Any published work which utilizes NAMD shall include the following reference Laxmikant Kale Robert Skeel Milind Bhandarkar Robert Brunner Attila Gursoy Neal Krawetz James Phillips Aritomo Shinozaki Krishnan Varadarajan and Klaus Schulten NAMD2 Greater scalability for parallel molecular dynamics J Comp Phys 151 283 312 1999 Electronic documents will include a direct link to the official NAMD page http www ks uiuc edu Research namd One copy of each publication or report will be supplied to Illinois through Dr Gila Budescu at the addresses listed below in Contact Information 7 Should Licensee wish to make commercial use of the Software Licensee will contact Illinois namd ks uiuc edu to negotiate an appropriate license for such use Commercial use includes 1 integration of all or part of the
115. llOrigin parameter 61 checkpoint command 16 COMmotion parameter 46 consexp parameter 53 consforcefile parameter 66 conskcol parameter 53 conskfile parameter 53 consref parameter 53 constantforce parameter 66 constraints parameter 53 coord psfgen command 37 coordinates parameter 19 coordpdb psfgen command 37 coorfile command 16 cutoff parameter 43 cwd parameter 20 cylindricalBC parameter 59 cylindricalBCAxis parameter 60 cylindricalBCCenter parameter 60 110 cylindricalBCexp1 parameter 60 cylindricalBCexp2 parameter 61 cylindricalBCk1 parameter 60 cylindricalBCk2 parameter 60 cylindricalBCll parameter 60 cylindricalBCl2 parameter 60 cylindricalBCr1 parameter 60 cylindricalBCr2 parameter 60 DCDfile parameter 21 DCDfreq parameter 21 DCDUnitCell parameter 21 delatom psfgen command 36 dielectric parameter 46 eField parameter 67 eFieldOn parameter 67 error message Atoms moving too fast 42 Bad global exclusion count 42 exclude parameter 46 ExcludeFromPressure parameter 66 ExcludeFromPressureCol parameter 66 ExcludeFromPressureFile parameter 66 extendedSystem parameter 61 fep parameter 86 fepCol parameter 86 fepEquilSteps parameter 86 fepFile parameter 86 fepOutFile parameter 87 fepOutFreq parameter 86 FFTWEstimate parameter 50 FFTWUseWisdom parameter 50 FFTWWisdomFile parameter 50 first psfgen command 35 firsttimestep parameter 43 fixedAtoms parameter 54 fixedAt
116. lowing faster distance checking and rigid bonds e hgroupCutoff A lt used for group based distance testing gt Acceptable Values positive decimal Default Value 2 5 Description This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother Warnings will be printed if this is not the case This value is also added to the margin e margin lt extra length in patch dimension A gt Acceptable Values positive decimal Default Value 0 0 Description An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system The value of this parameter will not 44 change the physical results of the simulation Unless you are very motivated to get the very best possible performance just leave this value at the default pairlistMinProcs lt min procs for pairlists gt Acceptable Values positive integer Default Value 1 Description Pairlists may consume a large amount of memory as atom counts densities and cutoff distances increase Since this data is distributed across processors it is normally only problematic for small processor counts Set pairlistMinProcs to the smallest number of processors on which the simulation can fit into memory when pairlists are used pairlistsPerCycle lt regenerate x times per cycle gt Acceptable Values positive integer Default Value 2 Description Rather than only regenerating the pairlist a
117. lues positive decimal Description Specifies barostat oscillation time scale for Langevin piston method If the instantaneous pressure did not fluctuate randomly during a simulation and the decay time was infinite no friction then the cell volume would oscillate with this angular period Having a longer period results in more averaging over pressure measurements and hence slower fluctuations in the cell volume A reasonable choice for the piston period would be 200 fs e LangevinPistonDecay lt damping time scale fs gt Acceptable Values positive decimal Description Specifies barostat damping time scale for Langevin piston method A value larger than the piston period would result in underdamped dynamics decaying ringing in the cell volume while a smaller value approaches exponential decay as in Berendsen s method above A smaller value also corresponds to larger random forces with increased coupling to the Langevin temperature bath Typically this would be chosen equal to or smaller than the piston period such as 100 fs e LangevinPistonTemp lt noise temperature K gt Acceptable Values positive decimal Description Specifies barostat noise temperature for Langevin piston method This should be set equal to the target temperature for the chosen method of temperature control e SurfaceTensionTarget lt Surface tension target dyn cm gt Acceptable Values decimal 65 Default Value 0 0 Description Specifies surface tens
118. m PDB file The same file used to generate the sequence is now read to extract coordinates In the residue ILE the atom CD is called CD1 in the pdb file so we use pdbalias atom to define the correct name If the segment names in the pdb file match the name we gave in the segment statement then we don t need to specify it again in this case we do specify the segment so that all atoms in the pdb file must belong to the segment 7 Build water segment Build a segment for the crystal waters The residue type for water depends on the model so here we alias HOH to TIP3 Because CHARMM uses an additional H H bond we must disable generation of angles and dihedrals for segments containing water Then read the pdb file 8 Read water coordinates from PDB file Alias the atom type for water oxygen as well and read coordinates from the file to the segment SOLV Hydrogen doesn t show up in crystal structures so it is missing from this pdb file 9 Guessing missing coordinates The tolopogy file contains default internal coordinates which can be used to guess the locations of many atoms hydrogens in particular In the output pdb file the occupancy field of guessed atoms will be set to 0 atoms which are known are set to 1 and atoms which could not be guessed are set to 1 Some atoms are poorly guessed if needed bond lengths and angles were missing from the topology file Similarly waters with missing hydrogen coordinates are given a def
119. mber of messages sent during PME 3D FFT by combining data into larger 104 messages to be transmitted along each dimension of either a 2D mesh or a 3D grid respectively While reducing the number of messages sent per processor from N to 2 sqrt N or 3 cbrt N the total amount of data transmitted for the FFT is doubled or tripled Extremely short cycle lengths less than 10 steps will also limit parallel scaling since the atom migration at the end of each cycle sends many more messages than a normal force evaluation Increasing pairlistdist from e g cutoff 1 5 to cutoff 2 5 while also doubling stepspercycle from 10 to 20 may increase parallel scaling but it is important to measure When increasing stepspercycle also try increasing pairlistspercycle by the same proportion 105 10 NAMD Availability and Installation NAMD is distributed freely for non profit use NAMD 2 5 is based on the Charm messaging system and the Converse communication layer http charm cs uiuc edu which have been ported to a wide variety of parallel platforms This section describes how to obtain and install NAMD 2 5 10 1 How to obtain NAMD NAMD may be downloaded from http www ks uiuc edu Research namd You will be re quired to provide minimal registration information and agree to a license before receiving access to the software Both source and binary distributions are available 10 2 Platforms on which NAMD will currently run NAMD should b
120. meter 52 movingConstraints parameter 67 movingConsVel parameter 68 MTSAlgorithm parameter 51 multiply psfgen command 36 mutate psfgen command 35 nonbondedFreq parameter 51 numsteps parameter 43 output command 15 outputEnergies parameter 22 outputMomenta parameter 22 outputname parameter 20 outputPairlists parameter 45 outputPressure parameter 22 outputTiming parameter 22 pairInteraction parameter 89 pairInteractionCol parameter 90 pairInteractionFile parameter 89 pairInteractionGroupl1 parameter 90 pairInteractionGroup2 parameter 90 pairInteractionSelf parameter 90 pairlistdist parameter 44 pairlistGrow parameter 45 pairlist MinProcs parameter 45 pairlistShrink parameter 45 pairlistsPerCycle parameter 45 pairlist Trigger parameter 45 parameters parameter 19 paraTypeCharmm parameter 19 paraTypeXplor parameter 19 parmfile parameter 23 patch psfgen command 35 pdb psfgen command 35 pdbalias atom psfgen command 37 pdbalias residue psfgen command 34 PME parameter 49 PMEGridSizeX parameter 49 PMEGridSizeY parameter 49 PMEGridSizeZ parameter 49 PMEInterpOrder parameter 49 PMEProcessors parameter 49 PMETolerance parameter 49 PRESSAVG 22 pressureProfileFreq parameter 91 pressureProfileNonbonded parameter 91 pressureProfileOn parameter 91 pressureProfileSlabs parameter 91 print command 15 psfcontext psfgen command 36 readexclusions parameter 23 readpsf psfgen command 37
121. meters 5 1 Non bonded interaction parameters and computations NAMD has a number of options that control the way that non bonded interactions are calculated These options are interrelated and can be quite confusing so this section attempts to explain the behavior of the non bonded interactions and how to use these parameters 5 1 1 Non bonded van der Waals interactions The simplest non bonded interaction is the van der Waals interaction In NAMD van der Waals interactions are always truncated at the cutoff distance specified by cutoff The main option that effects van der Waals interactions is the switching parameter With this option set to on a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance A graph of the van der Waals potential with this switching function is shown in Figure 1 If switching is set to off the van der Waals energy is just abruptly truncated at the cutoff distance so that energy may not be conserved switchdist cutoff A A AA energy o distance Figure 1 Graph of van der Waals potential with and without the application of the switching function With the switching function active the potential is smoothly reduced to 0 at the cutoff distance Without the switching function there is a discontinuity where the potential is truncated The switching function used is based on the X PLOR switching function The parameter switchdist spec
122. mines the dynamics of the system One always makes the changing potential depend on a coupling parameter A By convention can have values only in the range from 0 to 1 and a value 76 of A 0 corresponds to one defined state and a value of A 1 corresponds to the other defined state Intermediate values of A correspond to intermediate states in the case of conformational forcing calculations these intermediate states are physically realizable but in the case of molecular transformation calculations they are not The value of A is changed during the simulation In the first method provided here the change in A is stepwise while in the second method it is virtually continuous Multi configurational thermodynamic integration MCTI In MCTI one accumulates OU OA at several values of A and from these averages estimates the integral AA f OU OA dr With this method the precision of each OU OX can be estimated from the fluctuations of the time series of OU OA Slow growth In slow growth A is incremented by 6A 1 Nstep after each dynamics integration time step and the pmf is estimated as AA 0U 0A A Typically slow growth is done in cycles of equilibration at A 0 change to A 1 equilibration at AX 1 change to A 0 It is usual to estimate the precision of slow growth simulations from the results of successive cycles 6 7 3 Options for Conformational Restraints User supplied restraint and bounds spe
123. monic constraint force constant This parameter may specify any of the floating point fields of the PDB file either X Y Z occupancy or beta coupling temperature coupling Regardless of which column is used a value of 0 indicates that the atom should not be constrained Otherwise the value specified is used as the force constant for that atom s restraining potential 53 e selectConstraints lt Restrain only selected Cartesian components of the coordinates gt Acceptable Values on or off Default Value off Description This option is useful to restrain the positions of atoms to a plane or a line in space If active this option will ensure that only selected Cartesian components of the coordinates are restrained E g Restraining the positions of atoms to their current z values with no restraints in x and y will allow the atoms to move in the x y plane while retaining their original z coordinate Restraining the x and y values will lead to free motion only along the z coordinate e selectConstrX lt Restrain X components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian x components of the positions e selectConstrY lt Restrain Y components of coordinates gt Acceptable Values on or off Default Value off Description Restrain the Cartesian y components of the positions e selectConstrZ lt Restrain Z components of coordinates gt Acceptable Values on or off Default
124. n PDB file lt real name gt Residue name found in topology file Context Before reading sequence with pdb May call multiple times e segment lt segment ID gt lt commands gt Purpose Build a segment of the molecule A segment is typically a single chain of protein or DNA with default patches applied to the termini Segments may also contain pure solvent or lipid Arguments lt segment ID gt Unique name for segment 1 4 characters lt commands gt Sequence of commands in Tcl syntax to build the primary structure of the segment including auto first last residue pdb etc 34 Context After topology definitions and residue aliases May call multiple times Structure information is generated at the end of every segment command auto angles dihedrals none Purpose Override default settings from topology file for automatic generation of angles and dihedrals for the current segment Arguments angles Enable generation of angles from bonds dihedrals Enable generation of dihedrals from angles none Disable generation of angles and dihedrals Context Anywhere within segment does not affect later segments first lt patch name gt Purpose Override default patch applied to first residue in segment Default is read from topology file and may be residue specific Arguments lt patch name gt Single target patch residue name or none Context Anywhere within segment does not affect later segments l
125. namd ks uiuc edu If you discover and fix a problem not described in this manual we would appreciate if you would tell us about this as well so we can alert other users and incorporate the fix into the public distribution We are interested in making NAMD more useful to the molecular modeling community Your suggestions are welcome at namd ks uiuc edu We also appreciate hearing about how you are using NAMD in your work 1 4 Acknowledgments This work is supported by grants from the National Science Foundation BIR 9318159 and the National Institute of Health PHS 5 P41 RR05969 04 The authors would particularly like to thank the members of the Theoretical Biophysics Group past and present who have helped tremendously in making suggestions pushing for new features and testing bug ridden code 13 2 Getting Started 2 1 What is needed Before running NAMD explained in section 9 the following are be needed e A CHARMM force field in either CHARMM or X PLOR format e An X PLOR format PSF file describing the molecular structure e The initial coordinates of the molecular system in the form of a PDB file e A NAMD configuration file NAMD provides the psfgen utility documented in Section 4 which is capable of generating the required PSF and PDB files by merging PDB files and guessing coordinates for missing atoms If psfgen is insufficient for your system we recommend that you obtain access to either CHARMM or X PLOR both of which ar
126. nce of restart files rather than only the last version written binaryrestart lt use binary restart files gt Acceptable Values yes or no Default Value yes Description Activates the use of binary restart files If this option is set to yes then the restart files will be written in binary rather than PDB format Binary files preserve more accuracy between NAMD restarts than ASCII PDB files but the binary files are not guaran teed to be transportable between computer architectures The utility program flipbinpdb is provided with the Linux Intel version to reformat these files DCDfile lt coordinate trajectory output file gt Acceptable Values UNIX filename Description The binary DCD position coordinate trajectory filename This file stores the trajectory of all atom position coordinates using the same format binary DCD as X PLOR If DCDfile is defined then DCDfreq must also be defined DCDfreq lt timesteps between writing coordinates to trajectory file gt Acceptable Values positive integer Description The number of timesteps between the writing of position coordinates to the trajectory file The initial positions will not be included in the trajectory file DCDUnitCell lt write unit cell data to dcd file gt Acceptable Values yes or no Default Value no Description If this option is set to yes then DCD files will contain unit cell information in the style of Charmm DCD files velDCDfile lt velocity tr
127. nd 84 6 8 2 Implementation of free energy perturbation in NAMD 85 6 8 3 Example of an input file for running FEP alchemical transformations 87 6 8 4 Description of FEP simulation output 20 4 88 6 9 Locally Enhanced Sampling 88 6 9 1 Structure Generation ooo ee ee 88 0 9 2 SIMU ALIONS a o da a Be es ee ee 88 6 10 Pair Interaction Calculations 000000 eee 6 11 Pressure Profile Calculations 2 000000 eee ee 7 Translation between NAMD and X PLOR configuration parameters 8 Sample configuration files 9 Running NAMD 9 1 Individual Windows Linux Mac OS X or Other Unix Workstations 9 2 Linux Mac OS X or Other Unix Workstation Networks 9 3 Windows Workstation Networks 0 0 000 o 9 4 BProc Based Clusters Scyld and Clustermatic o ooo 9 5 Compaq AlphaServer SC 9 6 IBM ES 0000 82 ico a e EA OL Gis A A A NN 9387 Orig 20005 eN o is do li oe Hae 2 99 Memory Usage uti AA te a e 9 10 Improving Parallel Scaling o o a 10 NAMD Availability and Installation 10 1 How tovobtain NAMD corsa a a 10 2 Platforms on which NAMD will currently run o 103 Compiling NAMD La arar A A AA AA 10 4 Documentation 2 aa u aae a ae a epi e a E i ee References Index 93 95 100 100 101 102 102 103 103 103 103 104 104 106 106 106 106 107 108 110 List
128. ng the binaryrestart or binaryoutput options Note that in the current implementation at least the bincoordinates option must be used in addition to the coordinates option but the positions specified by coordinates will then be ignored e cwd lt default directory gt Acceptable Values UNIX directory name Description The default directory for input and output files If a value is given all filenames that do not begin with a are assumed to be in this directory For example if cwd is set to scr then a filename of outfile would be modified to scr outfile while a filename of tmp outfile would remain unchanged If no value for cwd is specified than all filenames are left unchanged but are assumed to be relative to the directory which contains the configuration file given on the command line 3 2 2 Output files e outputname lt output PDB file gt Acceptable Values UNIX filename prefix Description At the end of every simulation NAMD writes two PDB files one containing the final coordinates and another containing the final velocities of all atoms in the simulation This option specifies the file prefix for these two files The position coordinates will be saved to a file named as this prefix with coor appended The velocities will be saved to a file named as this prefix with vel appended For example if the prefix specified using this option was tmp output then the two files would be tmp output coor and tmp output vel e
129. o 200100030 A a a aa a LA Acknowledgements o s Lao ee Be AA A A AN Me oe ee bE Getting Started Dl Whats needed ati o a Bale a te eae ee AA ek 2 2 NAMD configuration fle 2 0 20 20 0002 ee ee 2 2 1 Configuration parameter syntax osooso e ee ee 2 2 2 Tel scripting interface and features ooo a 00200 00000 2 2 3 Required NAMD configuration parameters 004 Input and Output Files Sel bile formats sean vir Sale ie AN 31 1 PDB files o atoia a aed a a ee a Se a 3 1 2 X PLOR format PSF files a 3 1 3 CHARMM19 and CHARMM22 parameter files 314 DCD trajectory iles sip o ee A Ea Roe EAE ie oe ee AE 3 2 NAMD configuration parameters aooo e ee 32l Laput TIES an if tape tet Bila ae tt ee ote A edhe ote d 3 22 Output files inka a a eo Rao A A AAA a Be 3 23 Standard output soes Gis ase a hoe oe Ra RA oe as o 3 3 AMBER force field parameters a 3 4 GROMACS force field paramets 0 00000 eee ee eee Creating PSF Structure Files 41 Ordinary Usage eos aoe ee Gb eh A Dae ps a ana a 4 1 1 Preparing separate PDB files o o e o 4 1 2 Deleting unwanted atoms 0 0000 ee ee AD BPTI Example mi eg ee Rae le ee ea A eee ea ee a 4 3 Building solvent around a protein 2 0 ee ee 4 4 List of Commands 0 000 ee Basic Simulation Parameters 5 1 Non bonded interaction parameters and computations 5 1 1 Non bonded
130. odic cell parameters and extended system variables during the simulation If XSTfile is defined then XSTfreq must also be defined e XSTfreq lt how often to append state to XST file gt Acceptable Values positive integer Description Like the DCDfreq option controls how often the extended system configura tion will be appended to the XST file 61 e wrapWater lt wrap water coordinates around periodic boundaries gt Acceptable Values on or off Default Value off Description Coordinates are normally output relative to the way they were read in Hence if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for water molecules only e wrapAll lt wrap all coordinates around periodic boundaries gt Acceptable Values on or off Default Value off Description Coordinates are normally output relative to the way they were read in Hence if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output This option alters this behavior for all contiguous clusters of bonded atoms e wrapNearest lt use nearest image to cell origin when wrapping coordinates gt Acceptable Values on or off Default Value off Description Coordinates are normally wrapped to the diagonal unit cell centered on the origin This option combined with wrapWater or wrapA11 wraps coordinates to the nearest image to the ori
131. of appearance The script s should perform any required initialization on the Tcl interpreter including requesting data needed during the first timestep and define a procedure calcforces to be called every timestep At this point only low level commands are defined In the future this list will be expanded Current commands are e print lt anything gt This command should be used instead of puts to display output For example print Hello World e atomid lt segname gt lt resid gt lt atomname gt Determines atomid of an atom from its segment residue and name For example atomid br 2 N 71 e addatom lt atomid gt Request coordinates of this atom for next force evaluation and the calculated total force on this atom for current force evaluation Request remains in effect until clearconfig is called For example addatom 4 or addatom atomid br 2 N e addgroup lt atomid list gt Request center of mass coordinates of this group for next force evaluation Returns a group ID which is of the form gN where N is a small integer This group ID may then be used to find coordinates and apply forces just like a regular atom ID Aggregate forces may then be applied to the group as whole Request remains in effect until clearconfig is called For example set groupid addgroup 14 10 12 e clearconfig Clears the current list of requested atoms After clearconfig calls to addatom and addgroup can be used to
132. omsCol parameter 54 fixedAtomsFile parameter 54 fixedAtomsForces parameter 54 FMA parameter 48 FMAFFT parameter 48 FMAFFTBlock parameter 49 FMA Levels parameter 48 FMAMp parameter 48 FMAtheta parameter 48 freeEnergy parameter 74 freeEnergyConfig parameter 74 FullDirect parameter 50 fullElectFrequency parameter 51 GPRESSAVG 22 GPRESSURE 22 grocoorfile parameter 26 gromacs parameter 25 grotopfile parameter 25 guesscoord psfgen command 37 hgroupCutoff A parameter 44 IMDfreq parameter 71 IMDignore parameter 71 IMDon parameter 70 IMDport parameter 70 IMDwait parameter 71 lambda parameter 86 lambda2 parameter 86 langevin parameter 56 langevinCol parameter 56 langevinDamping parameter 56 langevinFile parameter 56 langevinHydrogen parameter 56 LangevinPiston parameter 65 LangevinPistonDecay parameter 65 LangevinPistonPeriod parameter 65 LangevinPistonTarget parameter 65 LangevinPistonTemp parameter 65 langevinTemp parameter 56 last psfgen command 35 les parameter 88 lesCol parameter 89 lesFactor parameter 89 lesFile parameter 89 longSplitting parameter 51 margin parameter 44 margin violations 41 maximumMove parameter 56 measure command 16 minBabyStep parameter 55 minimization parameter 55 111 minimize command 15 minLineGoal parameter 55 minTinyStep parameter 55 MISC energy 22 molly parameter 52 mollyIterations parameter 52 mollyTolerance para
133. onal performance may be gained by building NAMD against an SMP version of Charm such as net linux smp or net linux smp icc This will use a communication thread for each process to respond to network activity more rapidly For dual processor clusters we have found it that running two separate processes per node each with its own communication thread is faster than using the charmrun ppn option to run multiple worker threads However we have observed that when running on a single hyperthreaded processor i e a newer Pentium 4 there is an additional 15 boost from running standalone with two threads namd2 p2 beyond running two processors charmrun namd2 local p2 For a cluster of single processor hyperthreaded machines an SMP version should provide very good scaling running one process per node since the communication thread can run very efficiently on the second virtual processor We are unable to ship an SMP build for Linux due to portability problems with the Linux pthreads implementation needed by Charm The new NPTL pthreads library in RedHat 9 fixes these problems so an SMP port can become the standard shipping binary version in the future On some large machines with very high bandwidth interconnects you may be able to in crease performance for PME simulations by adding either strategy USE_MESH or strategy USE_GRID to the command line These flags instruct the Charm communication optimization library to reduce the nu
134. ontext is the same as the current context Arguments lt context gt Context ID returned by psfcontext Context At any time 36 writepsf charmm x plor lt file name gt Purpose Write out structure information as PSF file Arguments charmm Use CHARMM format numbers for atom types x plor Use X PLOR format names for atom types the default format required by NAMD lt file name gt PSF file to be generated Context After all segments have been built and patched readpsf lt file name gt Purpose Read in structure information from PSF file and adds it to the structure It is an error if any segments in the PSF file already exist Arguments lt file name gt PSF file in X PLOR format names for atom types Context Anywhere but within segment pdbalias atom lt residue name gt lt alternate name gt lt real name gt Purpose Provide translations from atom names found in PDB files to proper atom names read in from topology definition files Proper names from topology files will be used in generated PSF and PDB files This command also exists under the deprecated name alias Arguments lt residue name gt Proper or aliased residue name lt alternate name gt Atom name found in PDB file lt real name gt Atom name found in topology file Context Before reading coordinates with coordpdb May call multiple times coord lt segid gt lt resid gt lt atomname gt lt z y z gt Purpose Set coordinates fo
135. ou must be able to connect to each node via rsh ssh without typing your password this can be accomplished via a rhosts files in your home directory by an etc hosts equiv file installed by your sysadmin or by a ssh authorized_keys file in your home directory You should confirm that you can run ssh hostname pwd or rsh hostname pwd without typing a password before running NAMD Contact your local sysadmin if you have difficulty setting this up If you are unable to use rsh or ssh then add setenv CONV DAEMON to your script and run charmd or charmd faceless which produces a log file on every node You should now be able to try running NAMD as charmrun namd2 p lt procs gt lt configfile gt If this fails or just hangs try adding the verbose option to see more details of the startup process You may need to specify the full path to the namd2 binary Charmrun will start the number of processes specified by the p option cycling through the hosts in the nodelist file as many times as necessary You may list multiprocessor machines multiple times in the nodelist file once for each processor You may specify the nodelist file with the nodelist option and the group which defaults to main with the nodegroup option If you do not use nodelist charmrun will first look for nodelist in your current directory and then nodelist in your home directory Some automounters use a temporary mo
136. p alanin binaryoutput no DCDfreq 10 restartfreq 100 integrator params timestep 1 0 force field pa structure parameters exclude 1 4scaling switching switchdist cutoff pairlistdist stepspercycle rams alanin psf alanin params scaled1 4 1 0 on 8 0 12 0 13 5 20 96 This file shows another simple configuration file for alanin but this time with full electrostatics using PME and multiple timestepping protocol params numsteps 1000 initial config coordinates alanin pdb temperature 300K seed 12345 periodic cell cellBasisVectorl 33 000 cellBasisVector2 032 00 cellBasisVector3 O 0 32 5 output params outputname tmp alanin binaryoutput no DCDfreq 10 restartfreq 100 integrator params timestep 1 0 fullElectFrequency 4 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 full electrostatics PME on PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 32 97 This file demonstrates the analysis of a DCD trajectory file using NAMD The file pair pdb contains the definition of pair interaction groups NAMD will compute the interaction energy and force between these groups for each frame in the DCD file It is assumed that coordinate frames were written every 1000 timesteps See Sec 6 10 for more about pair interaction calculations initial config coor
137. psf files in X PLOR NAMD format e extracting sequence data from single segment PDB files e generating a full molecular structure from sequence data e applying patches to modify or link different segments e writing NAMD and VMD compatible PSF structure files e extracting coordinate data from PDB files e constructing guessing missing atomic coordinates e deleting selected atoms from the structure e writing NAMD and VMD compatible PDB coordinate files We are currently refining the interface of psfgen and adding features to create a complete molecular building solution We welcome your feedback on this new tool 4 1 Ordinary Usage psfgen is currently distributed in two forms One form is as a standalone program implemented as a Tcl interpreter which reads commands from standard output You may use loops variables etc as you would in a VMD or NAMD script You may use psfgen interactively but we expect it to be run most often with a script file redirected to standard input The second form is as a Tcl package which can be imported into any Tcl application including VMD All the commands available to the standalone version of psfgen are available to the Tcl package using psfgen within VMD lets you harness VMD s powerful atom selection capability as well as instantly view the result of your structure building scripts Examples of using psfgen both with and without VMD are provided in this document Generating PSF and PDB files for use with
138. r a single atom Arguments lt segid gt Segment ID of target atom lt resid gt Residue ID of target atom lt atomname gt Name of target atom lt xy z gt Coordinates to be assigned Context After structure has been generated coordpdb lt file name gt segid Purpose Read coordinates from PDB file matching segment residue and atom names Arguments lt file name gt PDB file containing known or aliased residues and atoms lt segid gt If specified override segment IDs in PDB file Context After segment has been generated and atom aliases defined guesscoord Purpose Guesses coordinates of atoms for which they were not explicitly set Calculation is based on internal coordinate hints contained in toplogy definition files When these are insufficient wild guesses are attempted based on bond lengths of 1 A and angles of 109 Arguments None Context After stucture has been generated and known coordinates read in writepdb lt file name gt Purpose Writes PDB file containing coordinates Atoms order is identical to PSF file generated by writepsf unless structure has been changed The O field is set to 1 for atoms with known coordinates 0 for atoms with guessed coordinates and 1 for atoms with no coordinate data available coordinates are set to 0 for these atoms 37 Arguments lt file name gt PDB file to be written Context After structure and coordinates are complete 38 5 Basic Simulation Para
139. r no Default Value no Description Pressure can be calculated using either the atomic virial and kinetic energy the default or a hydrogen group based pseudo molecular virial and kinetic energy The latter fluctuates less and is required in conjunction with rigidBonds SHAKE e useFlexibleCell lt anisotropic cell fluctuations gt Acceptable Values yes or no Default Value no Description NAMD allows the three orthogonal dimensions of the periodic cell to fluctuate independently when this option is enabled e useConstantRatio lt constant shape in first two cell dimensions gt Acceptable Values yes or no Default Value no Description When enabled NAMD keeps the ratio of the unit cell in the x y plane constant while allowing fluctuations along all axes The useFlexibleCel1 option is required for this option e useConstantArea lt constant area and normal pressure conditions gt Acceptable Values yes or no Default Value no Description When enabled NAMD keeps the dimension of the unit cell in the x y plane constant while allowing fluctuations along the z axis This is not currently implemented in Berendsen s method 6 5 1 Berendsen pressure bath coupling NAMD provides constant pressure simulation using Berendsen s method The following parameters are used to define the algorithm e BerendsenPressure lt use Berendsen pressure bath coupling gt Acceptable Values on or off Default Value off Description Specifies
140. r of timesteps between writing coordinates to the trajectory file NAMD Parameter velDCDfile X PLOR Parameter VELOcity Filename for the velocity trajectory file NAMD Parameter velDCDfreq X PLOR Parameter NSAVV Number of timesteps between writing velocities to the trajectory file NAMD Parameter numsteps X PLOR Parameter NSTEp Number of simulation timesteps to perform 94 8 Sample configuration files This section contains some simple example NAMD configuration files to serve as templates This file shows a simple configuration file for alanin It performs basic dynamics with no output files or special features protocol params numsteps 1000 initial config coordinates alanin pdb temperature 300K seed 12345 output params outputname tmp alanin binaryoutput no integrator params timestep 1 0 force field params structure alanin psf parameters alanin params exclude scaled1 4 1 4scaling 1 0 switching on switchdist 8 0 cutoff 12 0 pairlistdist 13 5 stepspercycle 20 95 This file is again for alanin but shows a slightly more complicated configuration The system is periodic a coordinate trajectory file and a set of restart files are produced protocol params numsteps 1000 initial config coordinates alanin pdb temperature 300K seed 12345 periodic cell cellBasisVectorl 33 000 cellBasisVector2 0 32 0 0 cellBasisVector3 00 32 5 output params outputname tm
141. riodic boundary conditions must also be enabled 90 e pressureProfileOn lt compute pressure profile gt Acceptable Values on or off Default Value off Description When active NAMD will compute kinetic and bonded contributions to the pressure profile Results will be recorded in the NAMD output file in lines with the format PRESSUREPROFILE ts Axx Ayy Azz Bxx Byy Bzz where ts is the timestep followed by the three diagonal components of the pressure tensor in the first slab the slab with lowest z then the next lowest slab and so forth NAMD will also output the pres sure profile averaged over all the steps since the last output The format of this line is PRESSUREPROFILEAVG ts Axx Ayy Azz ie exactly as for the instantaneous pres sure It is recommended to use the averaged pressure profile instead of the instantaneous value as this will give better statistics and may prevent artifacts when using multiple timestepping e pressureProfileSlabs lt Number of slabs in the spatial partition gt Acceptable Values Positive integer Default Value 10 Description NAMD divides the entire periodic cell into horizontal slabs of equal thickness pressureProfileSlabs specifies the number of such slabs e pressureProfileFreq lt How often to output pressure profile data gt Acceptable Values Positive integer Default Value 1 Description Specifies the number of timesteps between output of pressure profile data e pressurePro
142. rson Registration will be administered by the NAMD development team UNIVERSITY OF ILLINOIS NAMD MOLECULAR DYNAMICS SOFTWARE LICENSE AGREEMENT Upon execution of this Agreement by the party identified below Licensee The Board of Trustees of the University of Illinois Illinois on behalf of The Theoretical Biophysics Group TBG in the Beckman Institute will provide the molecular dynamics software NAMD in Executable Code and or Source Code form Software to Licensee subject to the following terms and conditions For purposes of this Agreement Executable Code is the compiled code which is ready to run on Licensee s computer Source code consists of a set of files which contain the actual program commands that are compiled to form the Executable Code 1 The Software is intellectual property owned by Illinois and all right title and interest in cluding copyright remain with Illinois Illinois grants and Licensee hereby accepts a restricted non exclusive non transferable license to use the Software for academic research and internal busi ness purposes only e g not for commercial use see Paragraph 7 below without a fee Licensee agrees to reproduce the copyright notice and other proprietary markings on all copies of the Soft ware Licensee has no right to transfer or sublicense the Software to any unauthorized person or entity However Licensee does have the right to make complimentary works that interoper
143. ry conditions aooo e a 58 6 4 2 Cylindrical harmonic boundary conditions 59 6 4 3 Periodic boundary conditions a 61 6 5 gt Pressure Control ao rana fe hk he ahs he tle A A oe a Se doe A 62 6 5 1 Berendsen pressure bath coupling o e e 63 6 5 2 Nos Hoover Langevin piston pressure control 64 6 6 Applied Forces and Analysis 66 6 64 Gonstant Forces ne ena A A A A A A eee o 66 6 6 2 External Electric Field 2 2 o o 67 6 6 3 Moving Constraints pa a a a ea A a aE a a a 67 6 6 4 Rotating Constraints aos s e ee ep Sg ee el e A es 68 6 6 5 Steered Molecular Dynamics SMD o 69 6 6 6 Interactive Molecular Dynamics IMD 70 6 6 cl intertace ei a A E ee A a 71 6 7 Free Energy of Conformational Change Calculations 74 6 7 1 User Supplied Conformational Restraints 0 200004 75 6 7 2 Free Energy Calculations e 76 6 7 3 Options for Conformational Restraints 0 002000048 77 6 7 4 Options for ATOM Specification e 78 6 7 5 Options for Potential of Mean Force Calculation 78 0216 Examples G ara aa A BE Se AAA A A a de Te 79 6T Appendix pori a Pa be Bop A Bate ae Re e E 81 6 8 Alchemical Free Energy Perturbation Calculations 84 6 8 1 Introduction and theoretical backgrou
144. sed on particular periodic images of the interacting atoms conserve momentum and are translationally invariant When dealing with externally applied forces such as harmonic constraints fixed atoms and various steering forces NAMD bases its pressure calculation on the relative positions of the affected atoms in the input coordinates and assumes that the net force will average to zero over time For time periods during with the net force is non zero the calculated pressure fluctuations will include a term proportional to the distance to the affected from the user defined cell origin A good way to observe these effects and to confirm that pressure for external forces is handled reasonably is to run a constant volume cutoff simulation in a cell that is larger than 62 the molecular system by at least the cutoff distance the pressure for this isolated system should average to zero over time Because NAMD s impluse basd multiple timestepping system alters the balance between bonded and non bonded forces from every timestep to an average balance over two steps the calculated pressure on even and odd steps will be different The PRESSAVG and GPRESSAVG fields provide the average over the non printed intermediate steps If you print energies on every timestep you will see the effect clearly in the PRESSURE field The following options affect all pressure control methods e useGroupPressure lt group or atomic quantities gt Acceptable Values yes o
145. semble averaging This variable could be set to 1 to include all the configurations for ensemble averaging Yet it is recommended to update fepOutFile energies at longer intervals to avoid large correlation between consecutive configurations e fepOutFile lt FEP energy output filename gt Acceptable Values filename Default Value outfilename Description An output file named fepOutFile fep generated by NAMD contains the FEP energies dumped every fepOutFreq steps Note Free energy calculations that rely upon equation 3 make use of an average temperature which in principle should coincide with the value of the thermostat Rather than employing the computed average of T AAa is estimated with the target value of the temperature defined by the user It is therefore necessary to activate some constant temperature scheme to carry out FEP calculations 6 8 3 Example of an input file for running FEP alchemical transformations The following example illustrates the use of TCL scripting for running the alchemical FEP feature of NAMD fep on fepfile ion fep fepCol X fepOutfile ion fepout fepOutFreq 5 fepEquilSteps 5000 set step 0 0 set dstep 0 1 while step lt 0 9 lambda step set step expr stept dstep lambda2 step run 10000 Here the pdb file read by NAMD to extract the information about perturbed atoms is biotin fep The pertinent information is present in the X column The output file of the free en
146. simulation has become unstable bad global exclusion count or similar error happens later in the simulation then the dynamics have probably become unstable resulting in the system exploding apart Energies printed at every timestep should show an exponential increase This may be due to a timestep that is too long or some other strange feature Saving a trajectory of every step and working backwards in can also sometimes reveal the origin of the instability 5 2 Full electrostatic integration To further reduce the cost of computing full electrostatics NAMD uses a multiple timestepping integration scheme In this scheme the total force acting on each atom is broken into two pieces a quickly varying local component and a slower long range component The local force component is defined in terms of a splitting function The local force component consists of all bonded and van der Waals interactions as well as that portion of electrostatic interactions for pairs that are separated by less than the local interaction distance determined by the splitting function The long range component consists only of electrostatic interactions outside of the local interaction distance Since 42 the long range forces are slowly varying they are not evaluated every timestep Instead they are evaluated every k timesteps specified by the NAMD parameter fullElectFrequency An impulse of k times the long range force is applied to the system every k tim
147. sion 2 5 Improved Parallel Scaling and Serial Performance Load balancer and communication library improvements that allow NAMD to scale to 1000 or more processors on PSC s Lemieux are included in this release For more modest Linux clusters we now provide TCP versions that outperform traditional UDP for gigabit ethernet and all released Linux binaries are built with the Intel compiler for better performance on Pentium 4 and Xeon processors and no penalty for Pentium III or Athlon processors Finally the inner loop has been optimized to incorporate pairlists that are saved between steps and automatically adjusted Pairlists can be disabled to save memory via the pairlistMinProcs option Trajectory Reading and Interaction Energy Analysis A new coorfile command allows Tcl scripts to read coordinates from DCD files allowing energies and forces to be evaluated for a saved trajectory This is most usefully combined with the new pair interaction feature allowing the isolation of forces between two specified groups of atoms or within a single group 10 Improved Constant Pressure Simulation and Coordinate Wrapping Average pressure is calculated for steps between energy outputs Berendsen method uses average rather then instantaneous pressure Pressure contributions due to steering forces handled consis tently Ratio of first two basis vectors can be fixed for flexible cells Any connected fragment can be wrapped to the periodic cell on outpu
148. system cutoff simulation AMBER NAMD TITLE amp cntrl ntb 0 igb 2 non periodic use cutoff for non bond nstlim 1000 numsteps 1000 Num of total steps ntpr 50 outputEnergies 50 Energy output frequency ntwr 50 restartfreq 50 Restart file frequency ntwx 100 DCDfreg 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 0 temperature O Initial temp for velocity assignment cut 10 cutoff 10 switching off Turn off the switching functions scee 1 2 exclude scaled1 4 1 4scaling 0 833333 1 1 2 default is 1 0 scnb 2 0 scnb 2 This is default Send amber on Specify this is AMBER force field parmfile prmtop Input PARM file ambercoor inpcrd Input coordinate file outputname md Prefix of output files Example 2 Periodic boundary system PME NVE ensemble using SHAKE algorithm 24 AMBER TITLE amp cntrl ntc 2 ntf 2 NAMD SHAKE to the bond between each hydrogen and it mother atom rigidBonds all tol 0 0005 rigidTolerance 0 0005 Default is 0 00001 nstlim 500 numsteps 500 Num of total steps ntpr 50 outputEnergies 50 Energy output frequency ntwr 100 restartfreq 100 Restart file frequency ntwx 100 DCDfreg 100 Trajectory file frequency dt 0 001 timestep 1 in unit of fs This is default tempi 300 temperature 300 Initial temp for velocity assignment cut 9 cutoff 9 switching off Turn off the switching functions amp end
149. t output 6PTI_water pdb 2 Embed the psfgen commands in this script psfgen lt lt ENDMOL 3 Read topology file topology toppar top_al122_prot inp 4 Build protein segment segment BPTI 29 pdb output 6PTI_protein pdb 5 Patch protein segment patch DISU BPTI 5 BPTI 55 patch DISU BPTI 14 BPTI 38 patch DISU BPTI 30 BPTI 51 6 Read protein coordinates from PDB file pdbalias atom ILE CDi CD formerly alias atom coordpdb output 6PTI_protein pdb BPTI 7 Build water segment pdbalias residue HOH TIP3 formerly alias residue segment SOLV auto none pdb output 6PTI_water pdb 8 Read water coordinaes from PDB file pdbalias atom HOH 0 0H2 formerly alias atom coordpdb output 6PTI_water pdb SOLV 9 Guess missing coordinates guesscoord 10 Write structure and coordinate files writepsf output bpti psf writepdb output bpti pdb End of psfgen commands ENDMOL Step by step explanation of the script 1 Split input PDB file into segments 6PTI pdb is the original file from the Protein Data Bank It contains a single chain of protein and some PO4 and H2O HETATM records Since each segment must have a separate input file we remove all non protein atom records using grep If there were multiple chains we would have to split the file by hand Create a second file containing only waters 2 Embed the psfgen commands in this script Run the psfgen program taking ev
150. t rather than only wrapping water molecules Coordinates can be wrapped to the true nearest image for hexagonal or similar highly faceted periodic cells 1 2 NAMD and molecular dynamics simulations Molecular dynamics MD simulations compute atomic trajectories by solving equations of motion numerically using empirical force fields such as the CHARMM force field that approximate the actual atomic force in biopolymer systems Detailed information about MD simulations can be found in several books such as 1 14 In order to conduct MD simulations various computer programs have been developed including X PLOR 7 and CHARMM 6 These programs were originally developed for serial machines Simulation of large molecules however require enormous computing power One way to achieve such simulations is to utilize parallel computers In recent years distributed memory parallel computers have been offering cost effective computational power NAMD was designed to run efficiently on such parallel machines for simulating large molecules NAMD is particularly well suited to the increasingly popular Beowulf class PC clusters which are quite similar to the workstation clusters for which is was originally designed Future versions of NAMD will also make efficient use of clusters of multi processor workstations or PCs NAMD has several important features e Force Field Compatibility The force field used by NAMD is the same as that used by the programs CHARMM
151. t run the provided daemon charmd exe on every node listed in the nodelist file Using charmd_faceless rather than charmd will eliminate consoles for the daemon and node processes 9 4 BProc Based Clusters Scyld and Clustermatic Scyld and Clustermatic replace rsh and other methods of launching jobs via a distributed process space There is no need for a nodelist file or any special daemons although special Scyld or Clustermatic versions of charmrun and namd2 are required In order to allow access to files the first NAMD process must be on the master node of the cluster Launch jobs from the master node of the cluster via the command charmrun namd2 p lt procs gt lt configfile gt For best performance run a single NAMD job on all available nodes and never run multiple NAMD jobs at the same time You should probably determine the number of processors via a script for example on Scyld NUMPROCS bpstat u 1 charmrun namd2 p NUMPROCS lt configfile gt You may safely suspend and resume a running NAMD job on these clusters using kill STOP and kill CONT on the process group Queueing systems typically provide this functionality allowing you to suspend a running job to allow a higher priority job to run immediately If you want to run multiple NAMD jobs simultaneously on the same cluster you can use the charmrun options startpe and endpe to specify the range of nodes to use The master node 1 is always included unless
152. t the beginning of a cycle regenerate multiple times in order to better balance the costs of atom migration pairlist generation and larger pairlists outputPairlists lt how often to print warnings gt Acceptable Values non negative integer Default Value 0 Description If an atom moves further than the pairlist tolerance during a simulation initially pairlistdist cutoff 2 but refined during the run any pairlists covering that atom are invalidated and temporary pairlists are used until the next full pairlist regeneration All interactions are calculated correctly but efficiency may be degraded Enabling outputPairlists will summarize these pairlist violation warnings periodically during the run pairlistShrink lt tol 1 x on regeneration gt Acceptable Values non negative decimal Default Value 0 01 Description In order to maintain validity for the pairlist for an entire cycle the pairlist tolerance the distance an atom can move without causing the pairlist to be invalidated is adjusted during the simulation Every time pairlists are regenerated the tolerance is reduced by this fraction pairlistGrow lt tol 1 x on trigger gt Acceptable Values non negative decimal Default Value 0 01 Description In order to maintain validity for the pairlist for an entire cycle the pairlist tolerance the distance an atom can move without causing the pairlist to be invalidated is adjusted during the simulation Ev
153. ted based on individual atoms while GPRESSURE incor porates hydrogen atoms into the heavier atoms to which they are bonded producing smaller fluc tuations The TEMPAVG PRESSAVG and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output for the first step in the simulation they will be identical to TEMP PRESSURE and GPRESSURE e outputEnergies lt timesteps between energy output gt Acceptable Values positive integer Default Value 1 Description The number of timesteps between each energy output of NAMD This value specifies how often NAMD should output the current energy values to stdout which can be redirected to a file By default this is done every step For long simulations the amount of output generated by NAMD can be greatly reduced by outputting the energies only occasionally e outputMomenta lt timesteps between momentum output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each momentum output of NAMD If specified and nonzero linear and angular momenta will be output to stdout e outputPressure lt timesteps between pressure output gt Acceptable Values nonnegative integer Default Value 0 Description The number of timesteps between each pressure output of NAMD If specified and nonzero atomic and group pressure tensors will be output to stdout e outputTiming lt timesteps between timing output gt Acceptable V
154. teps to run overriding the now optional numsteps parameter which defaults to 0 and can be called repeatedly You can run 0 just to get energies e The minimize command is similar to run and performs minimization for the specified number of force evaluations e The output command takes an output file basename and causes coor vel and xsc files to be written with that name e Between run commands the reassign Temp rescale Temp and langevin Temp parameters can be changed to allow simulated annealing protocols within a single config file The useGroup Pressure useFlexibleCell useConstantArea useConstantRatio LangevinPiston Langevin Piston Target LangevinPistonPeriod LangevinPistonDecay LangevinPistonTemp Surface Ten sionTarget BerendsenPressure BerendsenPressureTarget BerendsenPressureCompressibil ity and BerendsenPressureRelaxationTime parameters may be changed to allow pressure equilibration The fixedAtoms and constraintScaling parameters may be changed to preserve macromolecular conformation during minimization and equilibration fixedAtoms may only be disabled and requires that fixed AtomsForces is enabled to do this 15 e The checkpoint and revert commands no arguments allow a scripted simulation to save and restore to a prior state e The reinitvels command reinitializes velocities to a random distribution based on the given temperature e The rescalevels
155. test new algorithms easily If you are contem plating a particular modification to NAMD you are encouraged to contact the developers at namd ks uiuc edu for guidance e Interactive MD simulations A system undergoing simulation in NAMD may be viewed and altered with VMD for instance forces can be applied to a set of atoms to alter or rearrange part of the molecular structure For more information on VMD see http www ks uiuc edu Research vmd e Load Balancing An important factor in parallel applications is the equal distribution of computational load among the processors In parallel molecular simulation a spatial decomposition that evenly distributes the computational load causes the region of space mapped to each processor to become very irregular hard to compute and difficult to generalize to the evaluation of many different types of forces NAMD addresses this problem by using a simple uniform spatial decomposition where the entire model is split into uniform cubes of space called patches 12 An initial load balancer assigns patches and the calculation of interactions among the atoms within them to processors such that the computational load is balanced as much as possible During the simulation an incremental load balancer monitors the load and performs necessary adjustments 1 3 User feedback If you have problems installing or running NAMD after reading this document please send a complete description of the problem by email to
156. th into a number of non physical intermediate A states or win 85 dows Separate simulations can be started for each window Alternatively the TCL scripting ability of NAMD can be employed advantageously to perform the complete simulation in a single run An example making use of such script is supplied at the end of this section The following keywords can be used to control free energy calculations aimed at alchemical transformations e fep lt Is alchemical FEP to be performed gt Acceptable Values on or off Default Value off Description Turns on Hamiltonian scaling and ensemble averaging for alchemical FEP e lambda lt Coupling parameter value gt Acceptable Values positive decimal between 0 0 and 1 0 Description The coupling parameter value determining the progress of the perturba tion The non bonded interactions involving the atoms vanishing in the course of the MD simulation are scaled by 1 lambda while those of the growing atoms are scaled by lambda e lambda2 lt Coupling parameter comparison value gt Acceptable Values positive decimal between 0 0 and 1 0 Description The lambda2 value corresponds to the coupling parameter to be used for sampling in the next window The free energy difference between lambda2 and lambda is calculated Through simulations at progressive values of lambda and lambda2 the total free energy difference may be determined e fepEquilSteps lt Number of equilibration steps in the
157. the skipmaster option is given The requested number of processes are assigned to nodes round robin as with other network versions or the ppn option can be used to specify the number of processes per node To limit the master node to one process use the singlemaster option 102 9 5 Compaq AlphaServer SC If your machine as a Quadrics interconnect you should use the Elan version of NAMD other wise select the normal MPI version In either case parallel jobs are run using the prun command as follows prun n lt procs gt lt configfile gt There are additional options Consult your local documentation 9 6 IBM RS 6000 SP Run the MPI version of NAMD as you would any POE program The options and environment variables for poe are various and arcane so you should consult your local documentation for rec ommended settings As an example to run on Blue Horizon one would specify poe namd2 lt configfile gt nodes lt procs 8 gt tasks_per_node 8 9 7 Cray T3E The T3E version has been tested on the Pittsburgh Supercomputer Center T3E To run on procs processors use the mpprun command mpprun n lt procs gt namd2 lt configfile gt 9 8 Origin 2000 For small numbers of processors 1 8 use the non MPI version of namd2 If your stack size limit is unlimited which DQS may do you will need to set it with limit stacksize 64M to run on multiple processors To run on procs processors call the binary directly
158. the patch grid remains the same size The workaround is to increase the margin parameter so that the simulation starts with fewer larger patches Restarting the simulation will also regenerate the patch grid In rare special circumstances atoms that are involved in bonded terms bonds angles dihedrals Al pairlist distance cutoff gt Figure 4 Depiction of the difference between the cutoff distance and the pair list distance The pair list distance specifies a sphere that is slightly larger than that of the cutoff so that pairs are allowed to move in and out of the cutoff distance without causing energy conservation to be disturbed or impropers or nonbonded exclusions especially implicit exclusions due to bonds will be placed on non neighboring patches because they are more than the cutoff distance apart This can result in the simulation dying with a message of bad global exclusion count If an atoms moving too fast simulation has become unstable bad global exclusion count or similar error happens on the first timestep then there is likely something very wrong with the input coordinates such as the atoms with uninitialized coordinates or different atom orders in the PSF and PDB file Looking at the system in VMD will often reveal an abnormal structure Be aware that the atom IDs in the Atoms moving too fast error message are 1 based while VMD s atom indices are 0 based If an atoms moving too fast
159. this feature e eFieldOn lt apply electric field gt Acceptable Values yes or no Default Value no Description Specifies whether or not an electric field is applied e eField lt electric field vector gt Acceptable Values vector of decimals x y z Description Vector which describes the electric field to be applied Units are kcal mol A e which is natural for simulations This parameter may be changed between run commands allowing a square wave or other approximate wave form to be applied 6 6 3 Moving Constraints Moving constraints feature works in conjunction with the Harmonic Constraints see an appropriate section of the User s guide The reference positions of all constraints will move according to F t To 0 1 A velocity vector Y movingConsVel needs to be specified The way the moving constraints work is that the moving reference position is calculated ev ery integration time step using Eq 1 where U is in A timestep and t is the current timestep i e firstTimestep plus however many timesteps have passed since the beginning of NAMD run Therefore one should be careful when restarting simulations to appropriately update the firstTimestep parameter in the NAMD configuration file or the reference position specified in the reference PDB file NOTE NAMD actually calculates the constraints potential with U k x xo and the force with F dk x xo where d is the exponent consexp The result is that
160. toward the center and a negative value will pull atoms away from the center e sphericalBCexp1 lt exponent for first potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for first boundary potential The only likely values to use are 2 and 4 e sphericalBCr2 lt radius for second boundary condition A gt Acceptable Values positive decimal Description Distance at which the second potential of the boundary conditions takes effect This distance is a radius from the center If this parameter is defined then spericalBCk2 must also be defined e sphericalBCk2 lt force constant for second potential gt Acceptable Values non zero decimal Description Force constant for the second harmonic potential A positive value will push atoms toward the center and a negative value will pull atoms away from the center e sphericalBCexp2 lt exponent for second potential gt Acceptable Values positive even integer Default Value 2 Description Exponent for second boundary potential The only likely values to use are 2 and 4 6 4 2 Cylindrical harmonic boundary conditions NAMD provides cylindrical harmonic boundary conditions These boundary conditions can consist of a single potential or a combination of two potentials The following parameters are used to define these boundary conditions e cylindricalBC lt use cylindrical boundary conditions gt Acceptable Values on or off 59 Default
161. uctuation control implemented using Langevin dynamics as in SE Feller Y Zhang RW Pastor and BR Brooks Constant pressure molecular dynamics simulation The Langevin piston method J Chem Phys 103 11 1995 The equations of motion are r p m e r p F e p gp R V 3Ve 64 e 3V W P Po gee Re W W 3NY kT lt R gt 2mgkT h T oscillationperiod lt R2 gt 2WgekT h Here W is the mass of piston R is noise on atoms and Re is the noise on the piston The user specifies the desired pressure oscillation and decay times of the piston and tempera ture of the piston The compressibility of the system is not required In addition the user specifies the damping coefficients and temperature of the atoms for Langevin dynamics The following parameters are used to define the algorithm e LangevinPiston lt use Langevin piston pressure control gt Acceptable Values on or off Default Value off Description Specifies whether or not Langevin piston pressure control is active If set to on then the parameters LangevinPistonTarget LangevinPistonPeriod LangevinPistonDecay and LangevinPistonTemp must be set e LangevinPistonTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Langevin piston method A typical value would be 1 01325 bar atmospheric pressure at sea level e LangevinPistonPeriod lt oscillation period fs gt Acceptable Va
162. unt directory which is prepended to the path returned by the pwd command To run on multiple machines you must add a pathfix option to your nodelist file For example group main pathfix tmp _mnt host alphal host alpha2 There are many other options to charmrun and for the nodelist file These are documented at in the Charm Installation and Usage Manual available at http charm cs uiuc edu manuals and a list of available charmrun options is available by running charmrun without arguments If your workstation cluster is controlled by a queueing system you will need build a nodelist file in your job script For example if your queueing system provides a HOST_FILE environment variable 101 set NODES cat HOST_FILE set NODELIST TMPDIR namd2 nodelist echo group main gt NODELIST foreach node nodes echo host node gt gt NODELIST end NUMPROCS 2 NODES charmrun namd2 p NUMPROCS nodelist NODELIST lt configfile gt Note that NUMPROCS is twice the number of nodes in this example This is the case for dual processor machines For single processor machines you would not multiply NODES by two Note that these example scripts and the setenv command are for the csh or tcsh shells They must be translated to work with sh or bash 9 3 Windows Workstation Networks Windows is the same as other workstation networks described above except that rsh is not available on this platform Instead you mus
163. w there may be bugs that are only present when running multiple threads You may want to try running with charmrun see below if you experience crashes For other multiprocessor workstations the included charmrun program is needed to run multiple namd2 processes The local option is also required to specify that only the local machine is being used charmrun namd2 local p lt procs gt lt configfile gt You may need to specify the full path to the namd2 binary 100 9 2 Linux Mac OS X or Other Unix Workstation Networks The same binaries used for individual workstations as described above can be used with charmrun to run in parallel on a workstation network The only difference is that you must provide a nodelist file listing the machines where namd2 processes should run for example group main host brutus host romeo The group main line defines the default machine list Hosts brutus and romeo are the two machines on which to run the simulation Note that charmrun may run on one of those machines or charmrun may run on a third machine All machines used for a simulation must be of the same type and have access to the same namd2 binary By default the rsh command remsh on HPUX is used to start namd2 on each node specified in the nodelist file You can change this via the CONV_RSH environment variable i e to use ssh instead of rsh run setenv CONV_RSH ssh or add it to your login or batch script Y
164. whether or not Berendsen pressure bath coupling is active If set to on then the parameters BerendsenPressureTarget BerendsenPressureCompressibility and BerendsenPressureRelaxationTime must be set and the parameter BerendsenPressureFreq can optionally be set to control the behavior of this feature 63 e BerendsenPressureTarget lt target pressure bar gt Acceptable Values positive decimal Description Specifies target pressure for Berendsen s method A typical value would be 1 01325 bar atmospheric pressure at sea level e BerendsenPressureCompressibility lt compressibility bar gt Acceptable Values positive decimal Description Specifies compressibility for Berendsen s method A typical value would be 4 57E 5 bar corresponding to liquid water The higher the compressibility the more volume will be adjusted for a given pressure difference The compressibility and the relaxation time appear only as a ratio in the dynamics so a larger compressibility is equivalent to a smaller relaxation time e BerendsenPressureRelaxationTime lt relaxation time fs gt Acceptable Values positive decimal Description Specifies relaxation time for Berendsen s method If the instantaneous pres sure did not fluctuate randomly during a simulation and the compressibility estimate was exact then the inital pressure would decay exponentially to the target pressure with this time constant Having a longer relaxation time results in more av
165. with the p option namd2 p lt procs gt lt configfile gt For better performance on larger numbers of processors we recommend that you use the MPI version of NAMD To run this version you must have MPI installed Furthermore you must set two environment variables to tell MPI how to allocate certain internal buffers Put the following commands in your cshre or profile file or in your job file if you are running under a queuing system setenv MPI_REQUEST_MAX 10240 setenv MPI_TYPE_MAX 10240 Then run NAMD with the following command mpirun np lt procs gt namd2 lt configfile gt 103 9 9 Memory Usage NAMD has traditionally used less than 100MB of memory even for systems of 100 000 atoms With the reintroduction of pairlists in NAMD 2 5 however memory usage for a 100 000 atom system with a 12A cutoff can approach 300MB and will grow with the cube of the cutoff This extra memory is distributed across processors during a parallel run but a single workstation may run out of physical memory with a large system To avoid this NAMD now provides a pairlistMinProcs config file option that specifies the minimum number of processors that a run must use before pairlists will be enabled on fewer processors small local pairlists are generated and recycled rather than being saved the default is pairlistMinProcs 1 This is a per simulation rather than a compile time option because memory usage is molecule dependent 9 10 Improvin
166. zer uses a sophisticated conjugate gradient and line search algorithm with much better performance than the older velocity quenching method The method of conjugate gradients is used to select successive search directions starting with the initial gradient which eliminate repeated minimization along the same directions Along each direction a minimum is first bracketed rigorously bounded and then converged upon by either a golden section search or when possible a quadratically convergent method using gradient information For most systems it just works e minimization lt Perform conjugate gradient energy minimization gt Acceptable Values on or off Default Value off Description Turns efficient energy minimization on or off e minTinyStep lt first initial step for line minimizer gt Acceptable Values positive decimal Default Value 1 0e 6 Description If your minimization is immediately unstable make this smaller e minBabyStep lt max initial step for line minimizer gt Acceptable Values positive decimal Default Value 1 0e 2 Description If your minimization becomes unstable later make this smaller minLineGoal lt gradient reduction factor for line minimizer gt Acceptable Values positive decimal Default Value 1 0e 4 Description Varying this might improve conjugate gradient performance 6 2 2 Velocity quenching parameters You can perform energy minimization using a simple quenching scheme While this algor

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