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