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

shivangi nangia shivangi.nangia at gmail.com
Mon Dec 12 19:56:37 CET 2016


I am carrying out replica exchange solute tempering (REST) using the FEP

For some reason on continuing my simulations, the .cpt file is not getting

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 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

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.


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