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
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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
- Two main dependencies of PMEOPA are Nvidia CUDA (https://developer.nvidia.com/cuda-downloads) and Intel Cilk++ (http://software.intel.com/en-us/articles/download-intel-cilk-sdk)
Binaries
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 PMEOPA which includes detailed installation and usage guide.