[gmx-users] Problem with gromacs in Cluster

Sainitin Donakonda saigro16 at gmail.com
Thu Apr 25 14:28:56 CEST 2013

Hey all,

I recently ran 20ns simulation of protein ligand complex on cluster i used
following script to run simulation

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o

mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8

*I saved this as MD.sh And then submited to cluster using following script*

#BSUB -J testgromacs             # the job's name/array job
#BSUB -W 120:00                       # max. wall clock time in hh:mm
#BSUB -n 8,8                          # number of processors Min,Max
#BSUB -o test/output_%J.log             # output file
#BSUB -e test/errors_%J.log             # error file
#BSUB -M 8192     #Memory limit in MB

echo "Started at `date`"

cd test

echo "Running gromacs test in `pwd`"


echo "Finished at `date`"

It gave result but when checked files .xtc and created RMSD plots in that
x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns..

Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF run
time limit.
Exited with exit code 140". i gave maximum cluster time 120 hours..still it
is not sufficient ..

Can any body tell me  how do it split script i such  that i will get all
20ns simulation

Thanks in advance ,


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