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

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

mpirun mdrun_mpi single precision parallel MPI executable
mpirun mdrun_mpi_d double precision parallel MPI exectable

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: