PMEOPA

PMEOPA

PMEOPA, a Parallel Molecular Energetics using Octree-based Pairwise Approximation, have been implemented in order to perform fast computation of molecular mechanical (Lennard-Jones and Coulombic) and generalized Born solvation energetics which run on commodity multi-core CPUs and GPUs.

Features

  • Supported computations
    • Lennard-Jones, Coulombic, molecular surface based effective Born radii, generalized Born polarization
    • For each terms,
      • parallel computation on GPUs using CUDA
      • parallel computation on multi-core using Cilk++
      • naive (n^2) computation for a comparison

References

R. Chowdhury and C. Bajaj
Algorithms for faster molecular energetics, forces and interfaces
ICES Technical Report 10-32, The University of Texas at Austin, 2010.

Dependencies

Binaries

Source

  * Currently the source code is distributed only for academic use. Users interested in commercial licensing should contact Jitendra Jain.
  * Request academic license
  * Download source

Library Usage

  • Here is the user guide for PMEOPA which includes detailed installation and usage guide.