ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

Zhang, Xiaohua; Sundram, Shiv; Oppelstrup, Tomas; Kokkila-Schumacher, Sara L.; Carpenter, Timothy S.; Ingólfsson, Helgi I.; Streitz, Frederick H.; Lightstone, Felice C.; Glosli, James N.

doi:10.1063/5.0014500

Title: ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

Journal Article · Thu Jul 23 00:00:00 EDT 2020 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/5.0014500· OSTI ID:1669229

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Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical and Life Sciences (PLS) Directorate
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Computing Directorate
IBM, Yorktown Heights, NY (United States). Thomas J. Watson Research Center

We have implemented the Martini force field within Lawrence Livermore National Laboratory’s molecular dynamics program, ddcMD. The program is extended to a heterogeneous programming model so that it can exploit graphics processing unit (GPU) accelerators. In addition to the Martini force field being ported to the GPU, the entire integration step, including thermostat, barostat, and constraint solver, is ported as well, which speeds up the simulations to 278-fold using one GPU vs one central processing unit (CPU) core. A benchmark study is performed with several test cases, comparing ddcMD and GROMACS Martini simulations. The average performance of ddcMD for a protein–lipid simulation system of 136k particles achieves 1.04 µs/day on one NVIDIA V100 GPU and aggregates 6.19 µs/day on one Summit node with six GPUs. The GPU implementation in ddcMD offloads all computations to the GPU and only requires one CPU core per simulation to manage the inputs and outputs, freeing up remaining CPU resources on the compute node for alternative tasks often required in complex simulation campaigns.

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Research Organization:: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); National Institutes of Health (NIH)

Grant/Contract Number:: AC52-07NA27344; JDACS4C

OSTI ID:: 1669229

Alternate ID(s):: OSTI ID: 1642324

Report Number(s):: LLNL-JRNL-810343; 1016751; TRN: US2204189

Journal Information:: Journal of Chemical Physics, Vol. 153, Issue 4; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 10 works

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
supercomputer
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proteins
MARTINI force field
lipid bilayer
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Title: ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

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