gromacs
Table of Content
Versions and Availability
About the Software
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.
Usage
A sample script to run GROMACS follows:
#!/bin/bash
#PBS -A your_allocation
#PBS -q checkpt
#PBS -l nodes=1:ppn=8
#PBS -l walltime=12:00:00
#PBS -V
#PBS -j oe
#PBS -N gromacs_test
# mdrun_d is the MPI version of mdrun.
export EXEC=mdrun_d
export WORKDIR=$PBS_O_WORKDIR
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
cd $WORKDIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS `which $EXEC` -s fws_em.tpr \
-o fws_em.trr -c fws_b4pr.pdb -e em.edr -g em.log
The script is then submitted using qsub:
$ qsub job_script
where job_script is the name you gave the script file.
▶ QSub FAQ?
Resources
Usefule links for running GROMACS with hybrid MPI and OpenMP.
Plesae refer to GROMACS 4.6.7 User Manual for running GROMACS with GPU.
Last modified: September 10 2020 11:58:50.