NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

2 Summary NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition coupled with a multithreaded, message-driven design which is shown to scale eeciently to multiple processors. Also, NAMD incorporates the Distributed Parallel Multipole Tree Algorithm for full electrostatic force evaluation in ON 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 illustrates the performance of NAMD.