GROMACS

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. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details).

To put the executables for GROMACS in your path, type the following:

setup gromacs

For optional graphing functionality, type the following:

setup grace

A hard copy manual is available in the Core, and there are a demonstration and some examples available to be copied from the subdirectories in $GROMACS_TUTORIAL.