[gmx-users] check point file corrupted - umbrella sampling

Poojari, Chetan c.poojari at fz-juelich.de
Tue Sep 20 14:51:42 CEST 2011

Hello Justin,

Thank you very much for your reply.

I must hav used -cpo 0.cpt instead of -o 0.cpt.

Kind Regards,
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 20 September 2011 14:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] check point file corrupted - umbrella sampling

Justin A. Lemkul wrote:
> Poojari, Chetan wrote:
>> Hello Chris,
>> I followed the steps as mentioned in the umbrella sampling tutorial in
>> gromacs.
>> After NPT equilibration step, i did the umbrella simulation runs.
>> Below are the commands which i used:
>> grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n
>> index.ndx -o umbrella0.tpr
>> mdrun -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -s umbrella0.tpr
>> -o 0.cpt -c 0.gro -x 0.xtc
>> So, I had 24 such commands in my job submission script (one script i
>> had all the grompp command and in other script i had mdrun command)
>> for 24 windows, which  gave me 24 cpt files.
>> After the  final 24th window run, along with the output names
>> specified by me it also outputted default gromacs file names
>> state_prev.cpt, state.cpt, md.log, ener.edr.
>> Please can I know if its necessary to output even log files for these
>> 24 windows.
>> Size of the  state.cpt or the other cpt files which i got during npt
>> equilibration are 1.2 MB (these cpt files are okie when i do gmxcheck,
>> it does not give any error), where as of 24 different cpt files, each
>> has file size of 715MB. I had run simulations for 10ns on each window.
> Your command specifies "-o 0.cpt" so that's the problem.  The file 0.cpt
> is not a checkpoint, it is a trajectory.  The -o flag produces a .trr file.

More correctly, 0.cpt is not a *single* checkpoint, but rather a trajectory of
checkpoints, and though -o can produce such an output, it is typically reserved
for .trr output.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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