Created
June 16, 2015 06:22
-
-
Save leelasd/e5493d2fa663be53defc to your computer and use it in GitHub Desktop.
LSF script for running Gromacs in Grace
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
#BSUB -o . ## requests outfile be generated | |
#BSUB -a openmpi | |
#BSUB -q shared ## specify queue to run on, shared = default | |
#BSUB -J FAM ## job-name | |
#BSUB -W 24:00 ## walltime <HH:MM>= 24 hrs | |
#BSUB -n 4 | |
#BSUB -R "rusage[mem=50000]" ## memory limit= MB count only (1024MB = 1GB) | |
module load Apps/Gromacs | |
grompp -f em.mdp -c 267_fam_box.gro -p 267_fam_box.top -o em.tpr | |
mpirun.lsf mdrun_mpi -deffnm em | |
grompp -f nvt.mdp -c em.gro -p 267_fam_box.top -o nvt.tpr | |
mpirun.lsf mdrun_mpi -deffnm nvt | |
grompp -f npt.mdp -c nvt.gro -p 267_fam_box.top -o npt.tpr | |
mpirun.lsf mdrun_mpi -deffnm npt | |
grompp -f md_prod.mdp -c npt.gro -p 267_fam_box.top -o md_prod.tpr | |
mpirun.lsf mdrun_mpi -deffnm md_prod |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment