Gromacs

Gromacs is freely available and open source software.

Setting the module environment

A number of versions of Gromacs are available on the facility.

To set up the environment, when you log in, use (for example):

To add the executables for this specific version to your environment.

Alternatively:

Will add the executables for the default 4.6.3 version.

Executable naming conventions

The main executables available are :

mdrun single precision serial executable
mdrun_d double precision serial executable
mpirun mdrun_mpi single precision parallel MPI executable
mpirun mdrun_mpi_d double precision parallel MPI exectable

However, the naming convention for Gromacs versions below 4.6.3 are a little different:

mdrun.MPI single precision, parallel MPI 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. For more information look at the Gromacs homepage and at the Gromacs documentation.

Batch execution

Serial execution

An example script, example_serial.sh , looks like:

This requests 10 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 [...] 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 qsub options. The script can be submitted with:

Parallel execution

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

This requests 10 hours of runtime, to run in the current directory( -cwd ), using the current environment ( -V ), running on 4 cores ( -pe ib 4 ), using the double precision parallel version of mdrun, and where <options> 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 qsub options. The script can be submitted with: