Re: R: restart file

From: Chris Harrison (charris5_at_gmail.com)
Date: Sat Feb 25 2012 - 11:50:08 CST

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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