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MULTIHYDRO

1. platform e The previous released version was 2 October 2010 The change in this version is that temperature is expressed in centrigrades and some aspects of compatibility with version 10 of HYDRO The change in version 2 with respect to the previous one 1c of May 2005 was the inclusion of variable icase for type of hydrodynamic calculation as required by HYDRO program versions 8 and successive ones
2. several types e temp REAL Temperature Centigrade e eta0 REAL Solvent viscosity poise e rm REAL Molecular weight e vbar REAL Partial specific volume of solute g cm3 e solden REAL Solution density cm3 g e title CHARACTER 20 Title for the calculation up to 20 characters e filename CHARACTER 5 Generic file name to be user for output files with 5 characters not more or less e nconf INTEGER Number of conformations to be generated This section will have necessarily the format icase nu where means the user data NOTE rm is needed only for the calculation of the sedimentation coefficient and the intrinsic viscosity vbar and solden are needed only for the sedimentation coefficient Please see the HYDRO User s Manual as it is HYDRO the program that will do the hydrodynamic calculations 3 Specific user written section no 3 will contain data specific of the structure whose multiple conformations have to be generated Lengths sizes dimensions etc will be given in Angstrom units 4 General section no 4 initiates a Fortran DO loop over the conformations to be generated 5 Specific user written section no 5 will contain the specific instructions to construct each conformation with the information provided in Section 3 At the end of this section the number n of beads and the coordinates x i k k 1 2 3 i 1 n and radius e i of each bead must be defined Some generated s
3. this structure the bent or broken dumbbell The globules are represented by spheres of radii r and r2 The connector is represented by a string of nc beads of radius rs its total length is L 2ncr3 There are nj 1 beads in one of the arms 1 bead at the bent or hinge and nz beads at the second arm so that nc n m beads and the total number of beads in the model is n n n2 2 The conformation is determined by angle subtended second arm and the prolongation of the first one as indicated in the Figure The beads are placed in the x z plane with the first arm along the negative part of the z axis Thus the coordinates of beads i 1 n are 0 0 2 i 1 r3 and those of the first globule are 0 0 2 m1 1 r3 r1 The coordinates of the second arm and second globule are of the form pux O puz where ux sin and uz cos are the components of a unitary vector along the arm and p 2ir3 for the beads i 1 22 in the connector and p 2 nzr3 r2 for the second globule A number of conformations ncon 36 is generated with values of the angle in radians 0 ic 1 m nconf with ic l nconf or 0 S5 ic 1 in degrees for the 36 conformations Subroutine CHECK_OVERLAP is used to detect and reject conformations with overlapping beads MULTIHYDRO produces the input files for the HYDRO calculation on the accepted conformations that is done straightforwardly File summary txt from the HYDRO calculation can be readily inspect
4. File multihydro3 doc MULTIHYDRO Version 3 June 2011 Index 1 Introduction to MULTIHYDRO 2 Literature 3 Writing yourown MULTIHYDRO program 4 Output files Running HYDRO 5 Examples 6 Notes and hints 7 Release notes 1 Introduction to MULTIHYDRO MULTIHYDRO is a computer program that generates possible conformations of a particle providing a convenient interface with the HYDRO computer program so that the files for the calculations for all the conformations are automatically generated Essentially there are two general uses for MULTIHYDRO 1 Structural search of a rigid particle generating multiple possible conformations and facilitating the HYDRO calculation for each of them The user would later decide the ones that best fit some experimental data 2 Simulation of solution properties of a flexible particle As in the first case the user would provide the generation of the possible conformations and would also be in charge of doing the a posteriori averaging proper of the rigid particle In both cases the program has a friendly interface with HYDRO whose output summary txt file is a convenient for either search or averaging As described below MULTIHYDRO is supplied as a set of pieces of source code written in FORTRAN and it is intended to be a sample or template of the program that the user has to write for his her particular model 2 Literature The primary reference for MULTIHYDRO is e J Garcia de la
5. Torre A Ortega H E P rez Sanchez and J G Hernandez Cifre MULTIHYDRO and MONTEHYDRO Conformational search and Monte Carlo calculation of the solution properties of rigid and flexible bead models Biophys Chem 116 121 128 2005 The general primary reference for HYDRO is e J Garcia de la Torre S Navarro M C Lopez Martinez F G Diaz J Lopez Cascales HYDRO A computer software for the prediction of hydrodynamic properties of macromolecules Biophys J 67 530 531 1994 3 Writing your own MULTIHYDRO program As mentioned above the source code that we supplied for MULTIHYDRO is intended to be a template that you will employ to write the MULTIHYDRO program for your own case With this purpose in mind we have written the supplied MULHYDRO code in such a way that it contains e General sections that you must keep in your program without any modification and in the same place e Specific sections that the user will write and insert in the proper places within the code The purpose and placement of the sections look at the sample code are as follows 1 General section no contains comments declaration of variables used in other general sections 2 Specific user written section no 2 compulsory data contains values that the user has to supply for the following variables e icase INTEGER Type of hydrodynamic calculation in the HYDRO calculation Please consult the HYDRO manual for a description of the
6. ed or inserted in an Excel spreadsheet If the problem were a conformational search of the rigidly bent dumbbell in this case the determination of the bent angle could be done comparing the results with experimental data Another possibility is that of the flexibly hinged dumbbell For any property say p the final value is a conformational average over the values for the successive s of the form p X wx px X wx where wx is some statistical weight which would eventually contain an energetic and or a geometric contribution 6 Hints and notes This version of the program does not consider the calculation of scattering intensities distribution of distances and covolume and assumes that the full diffusion tensor is to be calculated Therefore it fills the file named hydro dat file with the required lines for the variables NH NS NTRIALS and IDIF with the values 0 0 O and 1 This is done in the lines of code WRITE 1 250 1 250 WRITE 1 250 WRITE 1 250 Poo oS These lines could be changed if these calculations are required In order to introduce your changes please consult the HYDRO User Guide for instructions on how this information must be provided 7 Release notes e This FORTRAN has been tested in two platforms a PC Windows with Visual Fortran 6 5 compiler and b Linux Red Hat 7 2 with g77 compiler The FORTRAN code is fully standard and therefore should compiled succesfully in any other
7. tructures could be perhaps rejected for reasons such as bead overlapping The criterion for rejection has to be programmed by the user Note that within section 6 we provide some utility subroutines for that purpose 6 General section no 6 is the last section in the program First it records the generated and eventually accepted conformation in the files required for the HYDRO calculation It also contains some utility subroutines that may be used not necessarily in the construction of the conformations of the user s model for purposes like checking bead overlap random number generator The code supply for MultiHydro will contain also general purpose subprograms Presently there is one to detect overlapping in an array of beads and another that generates conformations of a freely jointed chain 4 Ouput files Running HYDRO MULTHYDRO will produce the following files e One file named hydro dat which will be the main input data file for the subsequent HYDRO calculation e nconf files named xxxxx001 txt xxxxx002 txt etc where xxxxx is filename which will be structural files for the subsequent HYDRO calculation After running MULTIHYDRO you will run HYDRO to compute the hydrodynamic properties The procedure is very simple because you already have the input files hydro dat and xxxxx001 txt xxxxx002 txt etc Just launch the HYDRO executable and you will obtain the final results As this is a multi case HYDRO r
8. un the output file named summary txt will be particularly helpful This is a numeric archive containing nconf lines one for each conformation It has 13 columns containing 1 first 10 characters of title 2 translational diffusion coefficient 3 radius of gyration 4 volume 5 9 the five relaxation times 10 intrinsic viscosity 11 sedimentation coefficient 12 longest distance 13 covolume Afterwards you will have to analyze the set of values obtained for each individual conformation For this purpose you can open summary txt with an spreadsheet like EXCEL Similarly it can be easily read by a any user written programThe handling of this set of results The handling of the individual data will be according to your purpose when using MULTIHYDRO Some examples could be a In the structural search of a rigid particle you would plan to find the conformation whose properties are closest to available experimental data b If you are doing a Monte Carlo type calculation you will have to obtain the averages with the proper weights of the values of each property over all the generated conformations In both cases the tabular format of summary txt will be helpful For more details see the HYDRO Users s Guide 5 Example As an example of the use of MULTIHYDRO we present a case in which the structure being modeled has two globular domains connected by a rodlike connector with either a rigid bent or a flexible hinge we call

MULTIHYDRO

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