MOLECULAR MODELING: PROGRAM NAMD

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The simulation component of the MDScope modeling environment, NAMD [19], continues to undergo improvement in both features and speed*. The latest version, NAMD2 (a complete rewrite of much of the NAMD code), is nearing a public release. NAMD2 goes further than any previous release in achieving the NAMD design goals of modifiability, speed, and parallel performance. NAMD2 is more modifiable than the original version, as demonstrated by the features added in the last year. The program now supports periodic boundary conditions, using either cutoff electrostatics or full Ewald electrostatics. It allows larger simulation steps using a triple-time-stepping scheme, which can allow some simulations to run at double the speed of the original method. NAMD2 has a prototype TCL-based scripting interface that permits users to alter some parts of the simulation without having to look at the program code at all. It now also employs the DPME algorithm for full electrostatics, developed by our collaborators at Duke University. NAMD2 supports a large number of parallel machines, including clusters of workstations, the SGI Origin 200 and Origin 2000, the IBM SP3, the Convex Exemplar, and the Cray T3E. The new structure of the program exhibits improved sequential speed, and better parallel performance [22] on machines with dozens to hundreds of processors. Improved algorithms and parallel efficiency, and the availability of large numbers of processor have resulted in an order of magnitude increase in the speed of simulations.