NAMD:

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. The NAMD application is a recipient of a 2002 Gordon Bell Award. NAMD scales to hundreds of processors on high-end parallel platforms using gigabit ethernet. The NAMD has been ported to the Blue Gene and is extremely scalable. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

CMPD:

The CPMD (Car-Parrinello Molecular Dynamics) code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. The CMPD application has been ported and tested on the Blue Gene.