AMBER Archive (2003)

Subject: New program available: PMEMD (Particle Mesh Ewald Molecular Dynamics)

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 07 2003 - 16:13:33 CDT

We are proud to announce the release of version 3.00 (the first version to be
generally released) of PMEMD (Particle Mesh Ewald Molecular Dynamics).

PMEMD is a new version of the Amber module "Sander", and has been written with
the major goal of improving performance in Particle Mesh Ewald molecular
dynamics simulations and minimizations. The code has been totally rewritten in
Fortran 90, and is capable of running in either an Amber 6 or Amber 7 mode.
Functionality is more complete in Amber 6 mode, with the Amber 7 mode designed
mostly to do the same sorts of things that Amber 6 does, but with output that
is comparable to Amber 7 Sander. The calculations done in PMEMD are intended
to replicate either Sander 6 or Sander 7 calculations within the limits of
roundoff errors. The calculations are just done more rapidly in less memory,
and runs may be made efficiently on significantly larger numbers of
processors. Performance improvement ratios on Linux clusters and IBM SP3/4
clusters are typically in the range of 1.9 to 3.6 fold relative to Sander 6
and 1.5 to 3.8 fold relative to Sander 7. Memory requirements are roughly cut
in half. A large number of benchmarks are presented in the ReleaseNote file.

PMEMD was developed by Dr. Robert Duke in Prof. Lee Pedersen's Lab at
UNC-Chapel Hill, starting from the version of Sander in Amber 6. Funding
support was provided by NIH grant HL-06350 (PPG) and NSF grant 2001-0759-02
(ITR/AP). When citing PMEMD (Particle Mesh Ewald Molecular Dynamics) in the
literature, please use both the Amber Version 7 citation given in the Amber 7
manual, and the following citation:

Robert E. Duke and Lee G. Pedersen (2003) PMEMD 3, University of North
Carolina-Chapel Hill

PMEMD is available without charge to users who have an existing license for
Amber (version 6 or 7). For more information, and to download the code,
please go to:

                http://amber.scripps.edu/pme-get.html

..Robert Duke (UNC-Chapel Hill) and David Case (The Scripps Research
Institute)