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