GPU-Accelerated Exploration of Biomolecular Energy Landscapes
Published version
Peer-reviewed
Repository URI
Repository DOI
Type
Article
Change log
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
1549-9626
Volume Title
12
Publisher
American Chemical Society
Publisher DOI
Sponsorship
Engineering and Physical Sciences Research Council (EP/L504920/1)
EPSRC (Grant ID: EP/L504920/1)