Molecular dynamics simulator, with building and analysis tools

 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.