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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 20 14:44:29 CEST 2011

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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