[gmx-users] checkpoint file

[Juliette N.]

Thank you. I am using

 mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt

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,
> Matthias
>
> 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
>> frames.
>>
>>   *_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?
>>
>>
>> Thanks,
>
>
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-- 
Thanks,
J. N.