Computational Visualization Center

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

• Two main dependencies of PGBFOPA are Nvidia CUDA (https://developer.nvidia.com/cuda-downloads) and Intel Cilk++ (http://software.intel.com/en-us/articles/download-intel-cilk-sdk)

Binaries

• On Scientific Linux 6.3 with CUDA 4.2

Source

* Currently the source code is distributed only for academic use. Users interested in commercial licensing should contact licensing@otc.utexas.edu
* Request academic license
* Download source

Library Usage

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