PyGBe: Python on the surface, GPUs at the heart. BEM solver for Electrostatics of Biomolecules
Christopher Cooper
Lorena A. Barba
10.6084/m9.figshare.650855.v1
https://figshare.com/articles/poster/PyGBe_Python_on_the_surface_GPUs_at_the_heart_BEM_solver_for_Electrostatics_of_Biomolecules/650855
<p>Poster presented at the GPU Technology Conference, March 2013, San Jose, CA.</p>
<p>It presents the PyGBe code (pronounced 'pig-bee'), which solves the linearized Poisson-Boltzmann equation using a boundary element method, BEM. The underlying dense systems are solved using a Krylov-subspace method, accelerated with a treecode to achieve O(N log N) complexity. </p>
<p>The code presents a Python environment for the user, while computing all kernels in CUDA (interfaced with PyCuda), for maximum ease of use, combined with high performance on GPUs.</p>
<p><strong>Acknowledgement</strong></p>
<p>This research is made possible by a grant from the Office of Naval Research, Applied Computational Analysis Program (N00014-11-1-0356). LAB also acknowledges support from NSF CAREER award OCI-1149784.</p>
2013-03-13 23:24:59
GTC13
PyGBe
biomolecular electrostatics
GPU computing
python
Molecular Physics
Computational Biology
Computational Physics
Applied Computer Science
Biophysics