[gmx-users] replica exchange: checkpoint file not getting generated

[shivangi nangia]

Hi Mark,

Thanks.

Things work fine with Gromacs 2016.

Thanks,
Sxn

On Dec 12, 2016 4:49 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> We periodically hear reports of people unable to checkpoint reliably with
> some forms of replica exchange, but no clear pattern has emerged, and
> nobody has yet shared a set of inputs that reproduce. If you can reproduce
> it with GROMACS 2016, please open an issue at https://redmine.gromacs.org
> and
> share your input files and perhaps we can find a problem to fix.
>
> Mark
>
> On Tue, Dec 13, 2016 at 5:56 AM shivangi nangia <shivangi.nangia at gmail.com
> >
> wrote:
>
> > Hi,
> >
> > I am carrying out replica exchange solute tempering (REST) using the FEP
> > module.
> >
> > For some reason on continuing my simulations, the .cpt file is not
> getting
> > generated.
> >
> > I am confused why this might be happening as for the first run .cpt files
> > did get generated (so no possible mistake of -cpt being set to -1).
> >
> >
> > *The output options in my .mdp file are:*
> >
> > ; Output control
> >
> > nstxout                  = 500
> >
> > nstvout                  = 500
> >
> > nstfout                  = 0
> >
> > nstlog                   = 500
> >
> > nstenergy                = 500
> >
> >
> > *Commands that I am using:*
> >
> > set HOST = `hostname`
> >
> > set USER = `whoami`
> >
> > set indir=$SLURM_SUBMIT_DIR
> >
> > set workdir = $indir/$SLURM_JOB_ID
> >
> > set tpr = 2run
> >
> > set cptin = /shared/replica_exchange/solute_tempering/1run/1runcpt
> >
> > set outdir = $indir
> >
> > set outname = 2run
> >
> > set cpot = 2runcpt
> >
> >
> > srun  gmx_mpi mdrun  -s $tpr -deffnm $outname -cpi $cptin -multi 11
> > -replex 500 -dhdl dhdl_2run -cpo $cpot
> >
> >
> > I have also tried changing the default .cpt writing time from 15 minutes
> to
> > 1 minute by using the flag -cpt 1, the checkpoint file still does not get
> > generated.
> >
> > srun  gmx_mpi mdrun  -s $tpr -deffnm $outname -cpi $cptin -multi 11
> > -replex 500 -dhdl dhdl_2run -cpo $cpot -cpt 1
> >
> > I could not find any previous dicussions regarding such a problem.
> >
> > Kindly suggest.
> >
> > Thanks,
> > sxn
> > --
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