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 and is a community-driven project.

It is primarily designed for biochemical molecules like proteins, 
lipids and nucleic acids 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 and fluid dynamics.


Optional dependences:
For run-time detection of hardware capabilities set HWLOC=yes. This 
requires hwloc.
To enable MPI set PARALLEL=yes. This requires a MPI implementation 
either openmpi or mpich.
For enabling CUDA set CUDA=yes. This requires the CUDA SDK.
To enable OpenCL set OPENCL=yes. This requires a OpenCL 
implementation.