Announce: NAMD 1.5 released
david joseph hardy
dhardy at students.uiuc.edu
Sat Sep 5 19:38:08 EST 1998
Announcing the release of NAMD version 1.5
The Theoretical Biophysics group of the Beckman Institute at the
University of Illinois would like to announce the availability of
version 1.5 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
* Added features include rigid bonds and moving harmonic restraints.
* Updated user guide, also available in HTML form.
* Modified to work with PVM 3.4 beta.
* 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 ======================
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 Multipole 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.
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 Programming 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 Laboratory, 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 machines, which include HP, SGI, Sun,
and Linux, 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.
* UNIX with C and C++ compilers.
* PVM (http://www.epm.ornl.gov/pvm/pvm_home.html).
* For generating required PSF structure files, we recommend
Theoretical Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
namd at ks.uiuc.edu
September 4, 1998
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