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

DOE OSTI · 1669229

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.

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Abstract

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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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY MARTINI force field graphics processing units lipid bilayer molecular dynamics software proteins supercomputer

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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.. 2020-07-23. ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. https://doi.org/10.1063/5.0014500

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