namd - Not (just) Another Molecular Dynamics program

Abstract

The program namd is a parallel, object-oriented molecular dynamics program designed for efficiency, portability, and modularity. A general structure based on a small set of generic objects for communication between processors, calculation of atomic forces calculation, and integration of the equations of motion allows namd to adopt different algorithms for these aspects of the molecular dynamics calculation. The program uses a spatial decomposition to distribute atoms among processors. The model is broken down into uniform cubes of space referred to as patches. A set of patches are assigned to each processor. Patches are dynamically redistributed during the simulation to achieve better load-balancing. The program is message driven, meaning that the order of computation is determined by the arrival of messages indicating that the data necessary for a given computation is available. This type of scheduling of tasks allows for the greatest possible overlap of communication and computation times. namd uses the same force field and input files as the program X-PLOR and produces a binary DCD trajectory output file. As the simulation engine for the MDScope project it can be controlled by the visualization program VMD, which will allow for directed, interactive simulations. (For more information on VMD, see http://www.ks.uiuc.edu/Research/vmd/).

DateOfInformation

Thr Sep 25 16:08:47 1997

Domain

Scientific and Engineering Applications

Name

namd - Not (just) Another Molecular Dynamics program

Restrictions

namd is not public domain software. It is copyright by the Theoretical Biophysics Group and the University of Illinois, with all published and unpublished rights reserved. Permission is granted by the authors to use this software for noncommercial and nonprofit purposes. Commercial use of this software is prohibited without explicit consent from the namd developers. VMD IS PROVIDED ``AS IS'' WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

TargetEnvironment

namd is written in C++ and has been ported to HP, SGI, Sun, and IBM 6000s, the Exemplar, and the T3D.

Webpage

http://www.ks.uiuc.edu/Research/namd/

ContactIs

namd@ks.uiuc.edu