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GPU-Accelerated Exploration of Biomolecular Energy Landscapes

Published version
Peer-reviewed

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Authors

Mantell, RG 
Pitt, CE 
Wales, DJ 

Abstract

We present graphics processing unit (GPU)-acceleration of various computational energy landscape methods for biomolecular systems. Basin-hopping global optimization, the doubly nudged elastic band method (DNEB), hybrid eigenvector-following (EF), and a local rigid body framework are described, including details of GPU implementations. We analyze the results for eight different system sizes, and consider the effects of history size for minimization and local rigidification on the overall efficiency. We demonstrate improvement relative to CPU performance of up to 2 orders of magnitude for the largest systems.

Description

Keywords

Aldehyde Reductase, Algorithms, Apoptosis Regulatory Proteins, Humans, Molecular Dynamics Simulation, Myoglobin, Protein Structure, Tertiary, Proteins, Thermodynamics

Journal Title

Journal of Chemical Theory and Computation

Conference Name

Journal ISSN

1549-9618
1549-9626

Volume Title

12

Publisher

American Chemical Society
Sponsorship
Engineering and Physical Sciences Research Council (EP/L504920/1)
EPSRC (Grant ID: EP/L504920/1)
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