PGBFOPA

PGBFOPA

PGBFOPA, a Parallel Generalized Born Force using Octree-based Pairwise Approximation, have been implemented in order to perform fast computation of generalized Born polarization force with molecular surface-based formula using commodity multi-core CPUs and GPUs.

Features

  • Supported computations: atomic force for the generalized Born polarization with::
    • 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 PGBFOPA which includes detailed installation and usage guide.