NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

TLDR

NAMD is a high‑performance molecular dynamics program for large biomolecular systems on parallel computers. Built in C++ with an object‑oriented, spatial‑decomposition, multithreaded message‑driven architecture and a distributed parallel multipole tree algorithm, NAMD achieves efficient O(N) electrostatic calculations and supports interactive graphics integration. Benchmarking on a 32,867‑atom protein‑water system demonstrates NAMD’s performance capabilities.

Abstract

NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par allel multipole tree algorithm for full electrostatic force evaluation in O( N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illus trates the performance of NAMD.