NHSE Software Catalog

namd - Not (just) Another Molecular Dynamics program

url

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

record_maintainer

Andrew Dalke <dalke@ks.uiuc.edu>

date_of_information

Mon Jul 31 15:58:23 1995

review_level

Partially reviewed

version

1.0

pubdate

July 1, 1995

author

Mark Nelson, Bill Humphrey, Andrew Dalke, Attila Gursoy, Robert Brunner

contact

namd@ks.uiuc.edu

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/).

reference

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L.,
Skeel, R., Schulten, K., and Kufrin, R., "MDScope: A
Visual Computing Environment for Structural Biology"
Computer Physics Communications (1995). (In Press).

environment

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

copyright

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with all published and unpublished rights reserved.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.

comments

One of the goals of namd was to provide a molecular modelling
program which is easy to modify. To support this goal, the
namd source code is commented and a detailed Programmer's guide,
which documents the internal methods, algorithms, and classes,
is available at http://www.ks.uiuc.edu/Research/namd/prog_guide.ps .
Additionally, a user's guide is available at
http://www.ks.uiuc.edu/Research/namd/ug.ps.

keywords

application program; molecular biology