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Making molecular simulations run faster
Ramu Anandakrishnan, Tom Scogland, Andrew Fenley, John Gordon,
Wu Feng and Alexey V. Onufriev.
Accelerating Electrostatic Surface Potential Calculation with Multiscale
Approximation on Graphics Processing Units.
Journal of Molecular Graphics and Modelling,
28(8), 904-910, 2010.
Ramu Anandakrishnan and Alexey V. Onufriev.
An N log N approximation based on the natural
organization of biomolecules for speeding up the computation of
long range interactions
Journal of Computational Chemistry, 31(4), 691–706, 2010.
Long range electrostatic interactions play a critical role in thestructure, function and activity of biological molecules.
However the modeling of
electrostatic interactions is computationally intensive,
making it impractical to
simulate realistic systems for useful time-scales, even with today's fastest
supercomputers. We have developed a novel method,
hierarchical charge partitioning (HCP),for speeding up such computations. HCP has been implemented in the open source
molecular dynamics software NAB in Amber tools to deliver
up to 3 orders of magnitude speedup. HCP has also been ported to the GPU platfor
m (ATI and nvidia) for an additional
1-2 orders of magnitude speedup.