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. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend
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. cheers Fra 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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco frac...@myopera.com -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists