ANAFLEX INDEX
Contents
1. With a sampling frequency given by nfrec see above a conformation will be recorded from the trajectory file Thus the number of conformations per molecule that are recorded is the number of conformations per molecule in the trajectory nconf divided by nfrec nconf nfrec Then the total number of conformations recorded for graphics purposes nconfgraph will be that ratio multiplied by the number of molecules nmol plus 1 because the initail conformation is also taking into account nconfgraph nconf nconf nfrec 1 In general nconfgraph should be reasonably small say 11 51 101 Its maximum value is 999 The possible values of igraph are e igraph 1 pdb format is only valid when all the beads have the same same size if they are not an error message will be issued In this mode a series of files named xxxxxnnn pdb will be produced xxxxx is the five character string given for graphname and nnn will be a three digit index 001 002 up to nconfgraph If nconfgraph exceeds 999 there will be an error message As mentioned above you will typically ask for a moderate nconfgraph if not you will get so many files that may fill your disk The files xxxxxnnn pdb have a Protein Data Bank format and can be visualized using RasMol or similar molecular graphics tools With RasMol you can make Display Spacefill to view only the beads with the real size and also you can make Display Ball amp Stick to visualize the bead2. prop and error have the same meaning as in mode 1 and time is the value of time If mode 3 the file is empty The errors are estimated dividing the sample of nmol molecules in 5 subsamples therefore nmol must be a multiple of 5 File sumfile can be easily exported to Excel or other spreadsheets or graphics programs for further analysis or visualization of various aspects such as the dependence of properties on time external agents etc Other files In mode 1 or 2 if instprofiles 1 the program will produce files one file for each analyzed trajectory containing the instantaneous values of the properties for each individual molecule in the sample They serve to monitor how each individual molecule has evolved during the simulation These files are named fort 21 fort 22 etc They have blocks of lines one for each molecule Each block has the following data line time param fl param el prop1 prop2 prop3 These files are particularly useful for single molecule studies as they provide how the properties of a single molecule or each molecule in a sample evolve during the dynamics trajectory 7 Release notes e Version 3b is the third released version of ANAFLEX e In this version optimized mathematic libraries MKL are used to perform some vector and matrix operations
3. be the trajectory file in text format named trajectext The contents of this file will be e name of the inputfile main input file used in the BROWFLEX simulation e nmol I number of molecules or subtrajectories of a single molecule e ttraj R time of duration of the subtrajectory of each molecule e nconf I number of conformations per molecule or subtrajectory registered in the trajectory file including the initial one Thus it will be the number of conformations per molecule or subtrajectory that was specified as an input parameter for BROWFLEX plus 1 e N 1I number of beads atoms Then there will be nmol blocks of lines each containing nconf sub blocks of lines one for each recorded conformation with each sub block containing N lines each with the three values of the coordinates x y and z of each bead atom Note that the time interval between successive conformations is ttraj nconf A user supplied analysis program would open trajectext and read its information as indicated above It is likely that other information used by BROWFLEX could be needed As the name of the main input file used by BROWFLEX inputfile is provided the user program would open input file which contains the names of the other specific files where all the input data used by BROWF LEX are contained The output files listed below does not appear in mode 9 Log output file File Logfile will contain a description of the i
4. kk 11 are four integer numbers flags which are needed for some groups of properties If some or all of these values are not needed then fill them with zeros Make sure that the total number of properties sum over all of the groups is exactly the value given as nprops As it has been already mentioned the properties are grouped each group containing one or more than one property Each group has a code number The following table lists the groups and their properties Code for Number of Properties Description group properties 1 1 E IN 1 N linear end to end square distance 2 1 5 Square radius of gyration 3 1 G Component of the gyration tensor 4 2 Gxx Gyy Component of the gyration tensor 5 3 Gxy G Gye Component of the gyration tensor 7 2 ez e Extension along z and its square 8 4 ex x y ey Extension along x and y and their squares 12 1 An Birefringence FENE chain soft springs 13 1 lt P2 gt An P2 average over connectors hard springs 14 6 Teke tai Gee Tya Ta Components of the stress tensor 18 6 D n D D D Rs Rigid body hydrodynamic properties Flag ii 10 11 12 is the type of volume correction see observations below 20 5 R_ij 2 1 3 4 1 Powers of distance Rij between beads I and J given by unsing flags ii and jj 24 5 Psi psi 2 sin cos cos 2 Dihedral torsion angle rad subtended by beads I J K L given by us
5. may fail Static and animated VRML formats are among those considered by our separate visualization programs VisualBeads and MovieBeads Please see the User Guides for these programs igraph 8 MOVIE formats is valid for beads of arbitrarily different sizes This mode is intended for trajectories generated with nmol 1 or only in special cases with other nmol but such that the trajectory of a molecule is a continuation of that of the preceeding one In this mode a single file named xxxxx mov txt will be produced xxxxx is the five character string given for graphname This file contains a header with information on the beads and connectors and a series of snapshots each given by a block of lines one for each bead with the bead coordinates This format is intended to be handled offline with any other user supplied animated graphics program 6 Mode 9 Trajectory file This mode is just intended to transform the binary trajectory file generated by BROWF LEX into a text file that can be handled for any other user supplied program In this mode what has to be inserted in the main input file indicated as block b SECOND PART above is a single line containing trajectext the user supplied name of the text formatted trajectory file The content of this file is described below 7 Output files Trajectory file in text format In mode 9 i e when the user intends to use his her own analysis program the only output file will
6. File anaflex 3b pdf ANAFLEX Version 3b January 2014 INDEX Introduction and main input file Mode 1 Steady state properties Mode 2 Time dependent properties Mode 3 Correlation functions Mode 4 Visualization Mode 9 Trajectory Output files Release notes OO el Od oe 1 Introduction and main input file This program is intended for the analysis of the Brownian dynamics trajectories generated by BROWFLEX It can work in one of the following five ways working modes 1 Steady state calculation This is intended for steady state values of the observable properties which will be obtained as averages over the whole trajectory of the instantaneous values of the properties of a single molecule 2 Time dependent calculation This is intended for tracking the time evolution of properties of a sample of molecules At each time the sample average will be determined thus obtaining the time evolution of the properties of the sample 3 Correlation function calculation This is intended to compute some usual time correlation functions and obtaine some relaxation times 4 Record coordinates for graphics display picture or movie 5 Convert the output binary trajectory file into a text file The program can process any number of cases in the same run The input data files are the main data file datafile and one or several trajectory files trajfilel trajfile2 When program ANAFLEX is launched it asks
7. bed in the following sections sections 2 3 4 5 6 c THIRD FINAL PART again general for all of the working modes e trajfilel name of first trajectory file not free format fill with spaces up to 30 characters e successive lines with other trajectory files if we are processing more than one e asterisk in place of trajf ile indicates end of file We recall that the trajectory file generated by an execution of BROWFLEX will contain a number nmol of subtrajectories in which the trajectory of a molecule has been subdivided or a number nmol of molecules for different user provided initial conformations 2 Mode 1 Steady state properties This mode is intended for systems in steady state Averages of the properties are evaluated for each subtrajectory If nmol is not 1 estimates of the errors will also be given In this mode the particular lines to be inserted in the main input file i e block b SECOND PART above are e ncodes nprops two comma separated values which are ncodes is the number of groups of properties or codes to be computed see below nprops is total number of properties to be computed i e total number of properties included in all of the groups considered in this run Then there will be a number ncodes of lines A line for each code group with e icode ii jj kk 11 i e five comma separated values where icode is the code number of each group see table below ii jj
8. ction It should be like 11 21 51 For multiexponential fits values larger than 21 are advised tmax is the maximum time reached in the calculation of the correlation function iii jjj are bead indices needed in some cases If not needed give 0 0 nvx is the number of values of vx needed in some cases If not needed give 0 vx 1 vx nvx values of vx if nvx is not zero otherwise they are omitted The correlation functions corresponding to the various values of indcorr are as follows indcorr Correlation function Observations 1 Overall translational diffusion Dt 5 lt P 2 cos8 gt for a vector joining two _ ili and jjj are the indices of the beads two beads 9 Depolarized dynamic light scattering 10 Polarized dynamic light scattering vq 1 are scattering vectors 14 lt Rij Rij gt where Rij is the vector iii and jjj are beads I and J joining beads I and J 15 First Rouse mode 16 Second Rouse mode The only function that needs vq values is polarized DLS indcorr 10 5 Mode 4 Visualization This mode is intended to visualize snapshots or movies of the trajectory generated by BROWFLEX using our visualization programs VisualBeads and MovieBeads or any other graphics program The block b SECOND PART above in the main input file has the following lines e igraph is a flag indicating the visualization mode e graphname is a character string with five neither
9. for the name of the main input file that contains all the information required as described below Main input data file The datafile contains the following lines a FIRST PART general for all of the working modes e logfile is the name of the output file containing error messages intermediate results and also some final results e resfile is the name of the output file containing final results e sumfile is the name of a tabular summary results file ready to be exported to spreadsheets or other programs e nfrec is the sampling frequency of the records in the trajectory file For instance if this value is 10 one out of 10 consecutive records in the trajectory file will be used for the statistical averages calculation e instprofiles if 1 then files with instantaneous values along time of each property will be written in the working directory These files will be named after the Fortran unit which will be 31 32 33 For example in Compaq Digital Fortran they appear as fort 31 fort 32 The succesive files are for the succesive trajectories analized in the same run of ANAFLEX e mode indicates the working mode of the program The five possible values are mode steady state properties mode 2 time dependent properties mode 3 correlation function mode 4 for graphical display mode 9 for converting the binary trajectory file into a text file b SECOND PART depending on the mode The lines in this block will be descri
10. ing flags iijj kk ll Zero is trans conformation Observations a The main direction of the external agent flow field is z b Group 13 property lt P gt is the birefringence An for a model of identical quasi rigid bonds Group 18 properties D n D D D and Rg are the translational diffusion coefficient intrinsic viscosity eigenvalues of rotational diffusion and mean square radius of gyration evaluated according to the rigid body treatment in which hydrodynamic properties of individual conformations are evaluated from a Kirwood Riseman calculation with hydrodynamic interaction like in the HY DRO program please see the HYDRO User manual Of the various options in HYDRO to treat the so called volume correction the one denoted as ICASE 12 full volume correction for D De D and adjusted volume correction for n is used Please see the HYDRO User manual for further reference This calculation takes a long computer time and therefore a large value of nfrec giving a small number of conformations for calculations is recommended 3 Mode 2 Time dependent transient properties This mode is intended for the evaluation of properties dependig on time The result output files will contain the values of average properties as a function of time For that purpose a sample of nmol independent molecules should have been simulated or in other words the simulation should have been repeated for nm
11. more nor less than five characters e colorsfile is the name up to 30 characters of a file with indices for colors of beads and connectors see below for valid colors You can ommit this file if you do not want special colors then in this line put a minus sign as the first and only character and the program will take a standard combination of colors Also this file should be ommited in certain igraph modes see below The content of colorsfile is a number of lines with the following information N the number of beads in the first line The following N lines consists of two values each one the bead index 1 N and the color index for that bead NBONDS the number of connectors The following NBONDS lines consists of two values each one the connector index 1 NBONDS and the color index for that connector Note that N and NBONDS must coincide with the values that were used in the moleculefile during the simulation otherwise an error message will be issued The valid color indices when igraph is 6 or 7 are 1 WHITE 2 RED 3 YELLOW 4 NAVY BLUE 5 GREEN 6 PINK 7 SKY BLUE We note that colorsfile is the file with colors of beads and bonds in the format valid for VisualBeads and MovieBeads It will be needed for the production of graphics files in the formats accepted by these programs In the present version these are the cases when igraph 6 or igraph 7 Types of recording igraph modes
12. nput parameters read from every one of the trajectories analyzed in a run the possible error messages and both intermediate and some final results Results output file File resfile will contain the final results including all the cases trajectories analyzed in a run If mode 3 correlation functions the file informs about the time dependence of the correlation function details of the correlation analysis multiexponential fits and final results relaxation times Summary output file File sumfile will contain a summary of the results The contents will depend on mode If mode 1 steady state there will be a series of lines one for each trajectory with the following comma separated values param f1l param el prop1 errorl prop2 error2 prop3 error3 where e param fl and param el are the first flow parameter and the first electric field parameter in the cases when there were any of this kinds of external agents If simulation was performed without files containing flow and electric parameters see BROWF LEX manual 9 0 appears as the value of param f1 or param el e prop is the property value and error is its error If mode 2 time dependent properties the file contains blocks of data one for each trajectory Each block contains a series of lines with the following non comma separated values line time param fl param el propl error prop2 error2 prop3 error3 where param
13. o1 initial conformations The block b SECOND PART above in the main input file is the same as in mode 1 since the same properties can be evaluated The difference is that now you get the time evolution of every property computed at every time as a sample average over the nmol molecules 4 Mode 3 Correlation functions This mode is intended for the evaluation of several time correlation functions C t For that purpose a long enough simulation at equilibrium with only one molecule nmol 1 should have been performed Alternatively if nmol is not one then the starting point of each molecule should be the end of the previous one see instructions for BROWFLEX so that the whole simulation is like the simulation of a single molecule in nmol succesive subtrajectories The block b SECOND PART above in the main input file consists of just one line with the following comma separated values e indcorr ian inbase ntimc tmax iii jjjnvx vx 1 vx nvx where indcorr indicates the type of correlation funcion see table below ian is the type of fitting of correlation function usually 3 except 1 for translation Possible values are 0 none 1 C t Qt 2 In C t cytcottc3t up to fourth degree 3 C t ajexp b t a2exp bet up to 5 exponentials optionally including a base line inbase is the indicator of base line in some types of fitting ntimc is the number of values points of the correlation fun
14. s with a reduced size and what is quite interesting the connectors e igraph 6 Static VRML format is valid for beads of arbitrarily different sizes In this mode a series of files named xxxxxnnn vrml will be produced xxxxx s the five character string given for graphname and nnn will be a three digit index 001 002 up to nconfgraph If nconfgraph exceeds 999 there will be an error message As mentioned above you will typically ask for a moderate nconfgraph if not you will get so many files that may fill your disk The files xxxxxnnn vrml contain the coordinates and radii of the spheres in a full VRML format For each image our program sets intelligently the camera lights etc Note that the viewpoint varies from one image to another e igraph 7 Animated VRML format is valid for beads of arbitrarily different sizes This mode is intended for trajectories generated with nmol 1 or only in special cases with other nmol but such that the trajectory of a molecule is a continuation of that of the preceeding one In this mode a single file named xxXxxx ani vrml will be produced xxxxx is the five character string given for graphname It will contain a number of snapshots equal to the number of files in the other modes determined by the number of conformations in the trajectory and the sampling frequency nfrec The number of snapshots should be reasonably high but not too much if it is too large the VRML viewer
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