[edit] GROMACS on the ITS HPC Cluster

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions that usually dominate simulations, many groups are also using it for research on non-biological systems, e.g. polymers. Version 3.3.3 is currently available on the Case ITS HPC cluster.

To use GROMACS, the environment needs to be modified by issuing the following command:

   module load gromacs

This will automatically load Intel run time library and modify the environment correctly to enable you to run GROMACS in the current login session or batch script but. Intel run time library is required for execution of the executable produced by intel compilers. This library should be loaded before running and compiling the programs with intel compilers. To load intel compilers and library in HPC cluster for other instances than using gromacs, issue following command:

    module load intel-f

For more information, including tutorials on how to use GROMACS for molecular dynamics, see the official GROMACS web site, especially the Tutorials page. There is also a lot of good information at the GROMACS Wiki page.

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