Introduction to PMEMD 3.1 (Particle mesh Ewald molecular dynamics)

PMEMD is a new version of Sander 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).

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

Here are the PMEMD Release Notes, and the update notes for version 3.1.

PMEMD Software License Agreement

This Agreement, effective today, is made by and between you (hereinafter referred to as the "Licensee") and the University of California concerning PMEMD, a software program for running molecular dynamics simulations of biomolecules, which includes source code and documentation, as well as any upgrades, modified versions, updates, additions, copies, or derivative works made by Licensee (hereinafter referred to as the "Software").

Terms and Conditions

1. A non-exclusive nontransferable perpetual license is granted to Licensees who already have a license for Amber (version 6 or 7) to install and use the Software. Users who do not have a current Amber license must obtain that first, before downloading or using PMEMD.

 

 

2. The Licensee agrees that all terms and conditions of the existing Amber license apply to PMEMD. (The Amber license agreement text can be found here.)

 

 

3. Licensee agrees that any scientific publication of results obtained with the Software will acknowledge its use by an appropriate citation as specified in the Release Notes.

 

 

Do you accept all the terms of the above License Agreement? If you choose "Decline", the download will not continue. To download and install PMEMD, you must accept this Agreement.

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