Overview

GROMACS is a package to perform molecular dynamics. For more information look at the official GROMACS webpage and at the GROMACS documentation

Running GROMACS

Setting up the environment

To add the appropriate executables to your environment, load the module of the desired version. For instance to load version 4.5.6 use:

$ module add gromacs/4.5.6

 

Executable naming conventions

The main executables available are :

mdrun single precision serial executable
mdrun.MPI single precision, parallel MPI executable
mdrun_d double precision serial executable
mdrun_d.MPI double precision, parallel MPI executable

There are also single/double precision versions of the tools that come with the application, with the same naming scheme as above.

Batch execution

 

Serial execution

An example submission script, example_serial.sh, looks like:

#$ -cwd -V 
# request 2 hours of runtime
#$ -l h_rt=02:00:00
mdrun_d  <args>

This requests two hours of runtime, to run in the current directory( -cwd) and using the current environment (-V), using the double precision version of mdrun, and where <args> represents the arguments to mdrun. More memory per core can be requested, 2Gb for instance, by adding the line#$ -l h_vmem=2G to the script. For more options look at other available qsub options. The script can be submitted with:

$ qsub example_serial.sh

 

Parallel execution

For the parallel version, an example script, example_parallel.sh will take the form:

#$ -cwd -V 
# request 10 hours of runtime
#$ -l h_rt=10:00:00
# request 16 cores
#$ -l np=16
mpirun mdrun_d.MPI <args>

This requests 10 hours of runtime, to run in the current directory( -cwd), using the current environment (-V), running on 16 cores (-l np=16), using the double precision parallel version ofmdrun, and where <args> represents the arguments to mdrun. For more options look at other qsub options and general script examples (see relevant tabs). The script can be submitted with:

$ qsub example_parallel.sh
Licensing information

GROMACS is Free Software available under the GNU General Public License.