GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.

Invoking GROMACS

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.



More information

 A sample batch job script for GROMACS

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:

  qsub GROMACS_job.com

The above is an MPI-based parallel job script.