[Announce] NAMD 1.4 released
dalke at ks.uiuc.edu
Tue Jul 2 15:50:21 EST 1996
Announcing version 1.4 release of NAMD
The Theoretical Biophysics group at the University of Illinois and
the Beckman Institute would like to announce the availability version
1.4 of the program NAMD, a high-performance molecular mechanics
program for simulating large biomolecular systems on parallel and
distributed computers. This software is being made available to the
molecular modeling community free of charge, and includes commented
source code, documentation for users and programmers, and precompiled
binaries for HP and SGI workstations.
New in this version are various splittings for multiple
timestepping, cleaning up of the source and documentation, and various
=============== Basic information about NAMD ======================
A more complete description of NAMD is available on the NAMD WWW home
The software itself is available via anonymous ftp in the directory:
(please see the README file in this directory for the latest version
Email questions to namd at ks.uiuc.edu.
Efficient full electrostatics:
NAMD incorporates the Distributed Parallel Multiple Tree Algorithm
(DPMTA) developed by the Scientific Computing Group at Duke University
to provide full electrostatic interactions in O(N) time. To further
reduce the computational cost, DPMTA is integrated using a multiple
timestep integration scheme which computes full electrostatic
interactions only periodically during the simulation.
To simulate large systems using many processors. Efficient
parallel design uses a spatial decomposition scheme coupled with
multithreaded, message-driven execution to achieve load balance and
overlap of communication with computation.
A major design goal of NAMD is to allow researchers to implement
new algorithms and techniques easily. To achieve this, the design and
implementation of NAMD is fully documented in a Programmer's Guide. To
achieve the highest degree of modularity and data abstraction, an
object-oriented design is used and NAMD is implemented in C++.
NAMD can run on different parallel machines and message-passing
systems. The first two implementations of NAMD use PVM (Parallel
Virtual Machine) from Oak Ridge National Laboratories and Charm++ , a
message-driven coordination language developed at UIUC.
Compatibility with X-PLOR:
The input and output files used by NAMD are identical to those
used by the program X-PLOR. Thus, simulations can easily be migrated
between the packages and the output of NAMD can be analyzed using
X-PLOR or any other tool built for these file formats.
Standard MD features:
Implementation of standard molecular dynamics features such as
energy minimization, velocity rescaling, spherical harmonic boundary
conditions, harmonic atom restraints, and Langevin dynamics.
namd at ks.uiuc.edu
July 2, 1996
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