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PMEMD (Particle mesh Ewald molecular dynamics) is a new version of Sander (the main molecular dynamics code within AMBER, that 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 relative to Sander 6 or Sander 7 depend on the hardware and number of processors being used. Memory requirements are roughly cut in half. A large number of benchmarks are presented in the updated notes for version 3.1 (see link below).
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).
Since the release of AMBER 8, PMEMD is part of the AMBER suite of codes. AMBER 8 is installed on HPCx.
HPCx users may access PMEMD. To access this packages you should mail the HPCx help desk and we will give you access to the executable.
Please refer to the AMBER 8 userguide for using the latest version of PMEMD.
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