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

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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