gromacs¶
Note
SCARF is migrating to the SLURM batch system, instructions on this page which refer to LSF commands, parameters or configuration do not apply to SLURM. Please see our SLURM page for more information.
RHEL7 Modules:
Description for gromacs:
Description from GROMACS website.
“GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.”
Using gromacs:
GROMACS can be run on the command line using an LSF job submission script Eg :
#!/bin/bash
#BSUB -n 4
#BSUB -o %J.o
#BSUB -e %J.e
#BSUB -W 60
#BSUB -x
#Load desired
module load gromacs/4.6.5
#
# Submit the job using mpirun
mpirun -lsf mdrun_mpi -s example.tpr
where example.tpr is a gromacs input file.
Submit using:
[me@scarf]$ bsub < jcl
Where jcl is the name of the job submission script file from above. When changing the number of processors to run on, be sure to change ‘bsub -n’ as well as ‘mpirun.lsf -np’
To monitor your jobs progress use the normal LSF batch commands E.g.:
[me@scarf]$ bjobs
or
[me@scarf]$ bjobs -l
Documentation for gromacs: