Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 8, Issue 9, Pages 2997-3002Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct300284c
Keywords
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Funding
- National Science Foundation [OCI-0910735, NSF1047875, NSF1148276, TGMCB090110]
- NSF XSEDE program
- University of California (UC Lab) [09-LR-06-117792]
- CUDA fellowship from NVIDIA
- NIH
- HHMI
- NBCR
- CTBP
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1020765] Funding Source: National Science Foundation
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [1148276] Funding Source: National Science Foundation
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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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