[gmx-users] Problem with gromacs in Cluster

Francesco fracarb at myopera.com
Thu Apr 25 14:58:08 CEST 2013

You can split the simulation in different part (for example 5 ns each),
every time you'll finish one you will extend it adding more time.

My cluster uses a different "script system" than yours so I can't help
with it, but basically you have to submit more than 1 job with different
command to execute:

1) first production 
mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
2) modify the tpr file 
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
3) next X ns 
mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
4) modify the tpr file 
5) production md
and so on

with qsub you can submit a depending job (-hold_jid) that will run only
when the previous step will finish, in your case there should be a
similar way to do it.



On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:
> 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
> md_test.tpr
> 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*
> #!/bin/bash
> #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`"
> echo
> cd test
> echo "Running gromacs test in `pwd`"
> ./MD.sh
> 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 ,
> Sainitin
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

  fracarb at myopera.com

More information about the gromacs.org_gmx-users mailing list