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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. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Itasca has GROMACS builds that utilize Platform MPI as well as Open MPI. While the Open MPI builds are easier to use, the binaries built with Platform MPI generally offer better performance. "module avail gromacs" entered on the command line will print the versions of GROMACS available on Itasca. Any modules with an "-ompi" suffix were built using Open MPI, while modules with no suffix or a "-pmpi" suffix were built with Platform MPI.
A sample submission script for a Platform MPI build is below. You must load the module you are using in your submission script in your .bashrc file for Platform MPI Gromacs jobs to function properly.
#!/bin/bash -l #PBS -l walltime=24:0:0 #PBS -l mem=64GB #PBS -l nodes=8:ppn=8 module load gromacs cd $PBS_O_WORKDIR mpirun -np 64 -hostfile $PBS_NODEFILE mdrun -s topol
It is not necessary to load any modules in your .bashrc file if using the Open MPI builds. A sample submission script that would run an Open MPI build of Gromacs 4.5.1 is below.
#!/bin/bash -l #PBS -l walltime=24:0:0 #PBS -l mem=64GB #PBS -l nodes=8:ppn=8 module load gromacs/4.5.1-ompi cd $PBS_O_WORKDIR mpirun mdrun -s topol
Labs and other systems
To run this software interactively in a Linux environment run the command:
module load gromacs