[gmx-users] query about resuming a crashed mdrun
mark.j.abraham at gmail.com
Thu Apr 13 11:02:21 CEST 2017
Your second command didn't use deffnm flag, so mdrun interpreted your
intent as wanting most of the files to be named as the default. The 2016
release series refuses to run your second command precisely because of the
ambiguity about whether you intend to append, change names, etc.
On Thu, 13 Apr 2017 08:35 abhisek Mondal <abhisek.mndl at gmail.com> wrote:
> I was running mpirun -np 1600 mdrun_mpi -deffnm npt on a protein and
> outputs were normal but the job crashed as not finished within given cpu
> Then I used mpirun -np 2048 mdrun_mpi -s npt.tpr -cpi npt.cpt to resume the
> run from previous checkpoint. But, a whole lot of new files are being
> created. I thought it would be appended in the previous files.
> Previous files: npt.trr, npt.edr, npt.log, npt.cpt, npt_prev.cpt
> Files generated after
> resuming: state.cpt, state_prev.cpt, traj.trr, md.log, ener.edr
> If I watch the md.log file, it shows DD step as if it has resumed from the
> last run. Did I made any mistakes there ? Am I going to get the whole
> trajectory information in parts ?
> I'm using gromacs-4.6.2
> Some suggestions will be highly appreciated.
> Thank you.
> Abhisek Mondal
> *Senior Research Fellow*
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
> *Kolkata 700032*
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