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PMD is a scalable, parallel program for the efficient simulation of the dynamics of biological macromolecules. PMD utilizes the Greengard/Rokhlin Fast Multipole Algorithm to allow the simulation of very large biological macromolecular systems without sacrificing the important long-range Coulomb interactions. The force field implemented by PMD is compatible to programs such as CHARMM, X-PLOR, GROMOS. Discover and others. Residue topology and parameter files suitable for X-PLOR can be used with PMD. Particularly, PMD can fully implement the CHARMM19 CHARMM22 force fields. PMD is also intrinsically and transparently parallel and suitable for running on a wide variety of parallel architectures, both shared memory and message passing (PVM or MPI).

Current Version:   ??

License Type:   Free

Home Site:

Source Code Availability:   Yes

Available Binary Packages:

  • Debian Package:   No
  • RedHat RPM Package:   No
  • Other Packages:   No

Targeted Platforms:

PMD runs without changes on a large number of UNIX workstations and can easily be adapted to others. Parallel implementations exist for the CM-5, the Intel Paragon and the Cray T3D. The author said PMD should work just fine under Linux though no one tried yet.

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