[gmx-users] checkpoint file
matthias.ernst2 at student.kit.edu
Mon Aug 13 21:51:58 CEST 2012
Am 13.08.2012 21:42, schrieb Juliette N.:
> Thank you. I am using
> mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
I see a "md_prev.cpt". If I presume correctly that this is for the
continuation of the crashed run: Why and did you read what I wrote?
> but I dont get any output and the issued command terminates in the terminal.
> Do I have to remove the -o -c -g -e -x flags from the command line?
> Appreciate your help,
> On 13 August 2012 15:28, Matthias Ernst <matthias.ernst2 at student.kit.edu> wrote:
>> Long story short: backup everything (since it's a backup, and hopefully you
>> won't need it), then use the [whatever].cpt file. You don't want to do work
>> twice, do you? If you use the [whatever]_prev.cpi file, you will calculate
>> some frames *again* that are already there.
>> If you use an up-to-date version of Gromacs (4.5.5 is the most recent one),
>> then the files will be continued and not overwritten. This is stated on the
>> page you already found (hint: "remaining output will be appended to the
>> existing files (energy, trajectory, log, etc).")
>> Good luck,
>> Am 13.08.2012 21:07, schrieb Juliette N.:
>>> Hello all,
>>> I am going to restart my crashed simulations, but I am not sure which
>>> of *_prev.cpt or *.cpt to use as they contain different written
>>> *_prev.cpt >>>> Last frame -1 time 7462.900
>>> *.cpt >>>> Last frame -1 time 7468.965
>>> Also on the gmx site it is stated that :
>>> Before doing anything, back up your files! Then use
>>> mdrun -s topol.tpr -cpi state.cpt
>>> What files do I need to back up? the edr. trr .. files that were
>>> written before crash? Is the new run going to overwrite the old files?
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