R: restart file

From: Namd Namd (namd_10_at_yahoo.com)
Date: Mon Feb 27 2012 - 01:57:04 CST

Dear All, Thanks for the replies. I wrote a restart conf file for my md simulations. Could you please examine the conf file in below and share your ideas if this is true ? paratypeCharmm  on   # 1 ns for 4000 record parameters  x.prm   structure              x.psf coordinates            x_.pdb outputName             x_out   set temperature    300 #temperature $temperature   # continuing a run set inputname x_restart binCoordinates $inputname.coor binVelocities $inputname.vel extendedSystem $inputname.xsc   firsttimestep      1012500  #last step of previous run   # Integrator Parameters timestep            1 # same value with previous conf file nonbondedFreq       1 fullElectFrequency  5 stepspercycle       10 rigidBonds          water       # Force-Field Parameters exclude           scaled1-4 1-4scaling  0.8333333 cutoff          23 switching       on switchdist      21 pairlistdist    28       # Constant Temperature Control nvt langevin            on    langevinDamping     5     langevinTemp        $temperature langevinHydrogen    off        #--- PBC     cellBasisVector1  45. 0.0  0.0 cellBasisVector2  0.0  45.  0.0 cellBasisVector3  0.0  0.0  90.   #--- PME   dielectric      1 PME             on PMEGridSizeX    50 PMEGridSizeY    50 PMEGridSizeZ    90     #--- Output & Restart   binaryoutput    no   binaryrestart   yes   restartname     x_outrestart DCDfile         x_out.dcd     restartfreq        250 dcdfreq            250 xstFreq            250 outputEnergies     250 forceDCDfreq       250 outputPressure     250 outputtiming       250     run 2012500       ________________________________ Kimden: Chris Harrison <charris5_at_gmail.com> Kime: Namd Namd <namd_10_at_yahoo.com> Kopya: Nicholas M Glykos <glykos_at_mbg.duth.gr>; Aron Broom <broomsday_at_gmail.com>; namd-l_at_ks.uiuc.edu; Chiara.cosenza <chiara.cosenza_at_unina.it> Gönderildiği Tarih: 25 Şubat 2012 19:50 Cumartesi Konu: Re: R: namd-l: restart file Dear "Namd Namd <namd_10_at_yahoo.com>" Add the below script to your namd conf file for a restart job.  Replace "MY_PREV_NAMD_OUTPUT" with the appropriate filename.  The script will read your *.restart.xsc file and determine for you the beginning timestep for a restart job.   I hope it doesn't need to be said: Don' t use the script for a non-restart job.  That would be ... not smart. proc get_first_ts { xscfile } {         set fd [open $xscfile r]         gets $fd         gets $fd         gets $fd line         set ts [lindex $line 0]         close $fd         return $ts } set currenttimestep [get_first_ts $MY_PREV_NAMD_OUTPUT.restart.xsc] firsttimestep   $currenttimestep         Best, Chris --  Chris Harrison, Ph.D.NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd      Voice: 773-570-6078 http://www.ks.uiuc.edu/~char                        Fax: 217-244-6078 On Sat, Feb 25, 2012 at 11:00 AM, Aron Broom <broomsday_at_gmail.com> wrote: yes, don't look in the log file, just open up the restart file and check at the timestep it was saved at > > > >On Sat, Feb 25, 2012 at 10:38 AM, Nicholas M Glykos <glykos_at_mbg.duth.gr> wrote: > > >> >> >>> you have to specify the last timestep written in the dcd file. >> >>You have to specify the timestep at which the restart files you are >>using were saved (which depends on the value of restartfreq). The frames >>written in the DCD _after_ the restart should be thrown away (at the >>DCD merging step). >> >> >> >> >>-- >> >> >>           Nicholas M. Glykos, Department of Molecular Biology >>    and Genetics, Democritus University of Thrace, University Campus, >> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, >>   Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/ >> >> > > > >-- >Aron Broom M.Sc >PhD Student >Department of Chemistry >University of Waterloo >Dear namd user in the first time step you have to specify the last timestep written in the dcd file.From log file you can know which is the last timestep written.I find useful the package catdcd that provides an easyway to know the numbers of frames in a dcd file(and not only this). >Moreover you have to comment the temperature. >Chiara  > >Inviato da Samsung Mobile > > >Namd Namd <namd_10_at_yahoo.com> ha scritto: > > > > >Dear All, >I want to prepare a restart conf file to restart my md simulations from the last step of the previous job. So I searched for the restart conf files from mail archive and tutorials. Some of them include “firsttimestep 0” and others include “firsttimestep last step in namd.log file”. How can I specify "firsttimestep" when restarting the simulation? I think that  if I specify "firsttimestep 0" I can  restart from  the last step of the previous job. Because I also determine binCoordinates,   binVelocities ,   extendedSystem and comment the temperature  . Is it true ? >Thanks for the help.   --  Chris Harrison, Ph.D.NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd     Voice: 773-570-6078 http://www.ks.uiuc.edu/~char                        Fax: 217-244-6078

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