What is "namd"

Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). It has been developed by the joint collaboration of the Theoretical and Computational Biophysics Group (TCB), and the Parallel Programming Laboratory (PPL), at the University of Illinois at Urbana–Champaign.

It was introduced in 1995 by Nelson et al. as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores.

NAMD is available as precompiled binaries and as source code, as freeware for non-commercial use by individuals, academic institutions, and corporations for in-house business uses.