GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
To access the default version of GROMACS on the HEC, simply type the command
module add gromacs
To see what other versions of GROMACS are currently available, type
module avail gromacs
For more details on the module command, see Using environment modules on the HEC.
GROMACS has been built to support double precision arithmetic, so all tools must be called with a _d suffix. To call the parallel (MPI) versions of GROMACS tools, add the suffix _mpi_d.
GROMACS batch jobs may be run by creating a batch job control script called (e.g. GROMACS_job.com) like the following:
#$ -S /bin/bash #$ -q parallel #$ -l nodes=1 #$ -l node_type=10Geth* source /etc/profile module add gromacs # Pre-processing (serial) grompp_d -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md.tpr # Run the MD simulation mpirun mdrun_mpi_d -deffnm md
The script is then submitted for running by typing:
The above is an MPI-based parallel job script.