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J Chem Theory Comput. 2012 Sep 11;8(9):2997-3002. Epub 2012 Jul 27.

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics.

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1
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, Urey Hall, La Jolla, California 92093-0365, United States.

Abstract

In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We combine aMD with the inherent power of graphics processor units (GPUs) and apply the implementation to the bovine pancreatic trypsin inhibitor (BPTI). A 500 ns aMD simulation is compared to a previous millisecond unbiased brute force MD simulation carried out on BPTI, showing that the same conformational space is sampled by both approaches. To our knowledge, this represents the first implementation of aMD on GPUs and also the longest aMD simulation of a biomolecule run to date. Our implementation is available to the community in the latest release of the Amber software suite (v12), providing routine access to millisecond events sampled from dynamics simulations using off the shelf hardware.

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