Poojari, Chetan wrote:
Hello Justin,
Thank you very much for your reply.
I must hav used -cpo 0.cpt instead of -o 0.cpt.
Are you saying the commands shown below are wrong? Using "-cpo 0.cpt" is indeed
the correct approach.
-Justin
Kind Regards,
chetan
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@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
--
========================================
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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========================================
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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