Parallel MD Program NAMD 2.0b2 Available

Jim Phillips jim at ks.uiuc.edu
Fri Oct 16 21:20:05 EST 1998


The Theoretical Biophysics Group at the University of Illinois is proud
to announce the public release of a new version of the parallel
molecular
dynamics simulation program NAMD.  NAMD2 is a major improvement over
its predecessor, NAMD 1.5, in both computation speed and simulation
features.

This release is a binary-only beta version of NAMD2.  It has already
received extensive testing inside our group, but we still have some
additional testing and code cleanup before releasing the source.
Nevertheless, we believe it to be stable, and think you will find it a
significant improvement over NAMD 1.5.

NAMD2 binaries for Linux, HP-UX, Solaris, SGI Origin and the T3E are
available at ftp://ftp.ks.uiuc.edu/pub/mdscope/namd2/bin/.  For more
information see http://www.ks.uiuc.edu/Research/namd/Namd2.html
and direct questions or comments to namd at ks.uiuc.edu.

----------------------------------------------------------------------

NAMD 2.0 New Features

- Supports periodic and non-periodic MD simulations.

- Can use DPME for full electrostatics for periodic simulations, and
DPMTA for non-periodic simulations.  Cutoff simulations are also
supported.

- Triple timestepping.

- Rigid bonds to hydrogen atoms.

- Fixed atoms (Atoms which are constrained not to move do not have
forces calculated for them).

- Berendsen and Langevin piston constant pressure methods.

- Steered Molecular Dynamics (SMD).

----------------------------------------------------------------------

Problems?

For problems or questions, send email to namd at ks.uiuc.edu.  If you
think you have found a bug, please include what machine you are
running on, and, if possible, a dump of the program output and/or a
copy of your input files.  As a beta release, we expect you will find
a few rough edges in the program or documentation.  Your feedback will
help us to fix these.

----------------------------------------------------------------------

NAMD2 Known Deficiencies

- NAMD2 will currently not run if the number of processors exceeds
the number of patches in the system.  This typically only results when
you use a large number of processors and a large cutoff.

- Do not use constant-pressure with multiple timestepping or rigid
bonds.

- DPME has not yet received extensive testing.

- NAMD2 requires the X-PLOR package to produce the .psf and .par input
files.  If you don't have X-PLOR, you probably can't use NAMD2 yet.
See http://xplor.csb.yale.edu/xplor-info/xplor-info.html for
information.

----------------------------------------------------------------------







More information about the X-plor mailing list