IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

NAMD (parallel molecular dynamics) 1.5 beta 6 available

david joseph hardy dhardy at students.uiuc.edu
Tue Jul 7 17:37:19 EST 1998

Announcing the release of NAMD version 1.5 beta 6

The Theoretical Biophysics group at the Beckman Institute, the 
University of Illinois would like to announce the availability of 
version 1.5 beta 6 of 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 and extensive documentation.  

New in this version
* Enhanced performance by as much as 30%.  
* Modified to work with the latest version of DPMTA (2.7).  
* Included DPMTA source to make installation easier.  
* Simplified build process, fewer options to specify, better documentation.  
* Several bug fixes.  

====================  Basic information about NAMD  ======================

Obtaining NAMD
A more complete description of NAMD is available on the NAMD home page:

The software itself is available via anonymous ftp in the directory:

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.

Scalable parallelism:
  NAMD has an efficient parallel design that allows large systems to 
  scale well to many processors.  The use of a spatial decomposition 
  scheme combined with message-driven execution achieves load balance 
  and the overlap of communication and computation.  

  A major design goal of NAMD is to allow researchers to implement new 
  algorithms and techniques easily.  To achieve this, NAMD design and
  implementation is fully documented in the NAMD Programmer's Guide.  
  NAMD has an object-oriented design implemented in C++ to provide a 
  high degree of modularity and data abstraction.  

  For communication, NAMD uses PVM (Parallel Virtual Machine) from 
  Oak Ridge National Laboratories, which has itself been ported to 
  most architectures.  Porting NAMD is then simply a matter of having 
  PVM and a reasonable C++ compiler.  We have successfully ported 
  NAMD to all of our UNIX computers, which include HP, SGI, and Sun, 
  both single processor and shared memory multiprocessor.  

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 be easily migrated 
  between the two packages, allowing the output of NAMD to be analyzed 
  using X-PLOR or any other tool built for these file formats.

Standard MD features:
  NAMD implements standard molecular dynamics features such as energy 
  minimization, velocity rescaling, spherical boundary conditions, 
  harmonic constraints, and Langevin dynamics.

Theoretical Biophysics Group 
NIH Resource for Macromolecular Modeling and Bioinformatics 
Beckman Institute for Advanced Science and Technology 
University of Illinois at Urbana-Champaign 

						David Hardy
						namd at ks.uiuc.edu
						July 7, 1998

More information about the Molmodel mailing list

Send comments to us at archive@iubioarchive.bio.net