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J Chem Theory Comput. 2013 Sep 10;9(9):3878-88. doi: 10.1021/ct400314y. Epub 2013 Aug 20.

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

Author information

1
San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States.
2
NVIDIA Corporation , 2701 San Tomas Expressway, Santa Clara, California 95050, United States.
3
Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States.

Abstract

We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.

PMID:
26592383
DOI:
10.1021/ct400314y

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