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

[Mark Abraham]

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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