GROMACS (Groningen MAchine for Chemical Simulation) is a free package for molecular dynamics simulations.  It comes as a part of the Rocks Bio Roll, and is available on all HPC nodes.  It has been compiled with mpi (MPICH) support.

Using GROMACS on HPC

GROMACS' Rock Bio Roll documentation just points to GROMACS's home site where you can find complete documentation and reference manuals. The other links there are no longer correct.  Tutorials are also available on HPC at /opt/Bio/gromacs/share/tutor.