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. 2019 Jan:1:100004.
doi: 10.1016/j.rechem.2019.100004. Epub 2019 Jun 20.

Virial Based Berendsen Barostat on GPUs using AMOEBA in Tinker-OpenMM

Matthew Harger  1 , Pengyu Ren  1
Affiliations

Virial Based Berendsen Barostat on GPUs using AMOEBA in Tinker-OpenMM

Matthew Harger et al. Results Chem. 2019 Jan.

Abstract

The Tinker-OpenMM package for AMOEBA molecular dynamics on GPU has long been limited to the Monte Carlo barostat due to the lack of virial calculation. In this paper, we report the calculation of the internal virial for the AMOEBA forcefield. This constitutes the first GPU implementation of a polarizable internal virial. This is followed by the implementation of the Berendsen barostat into Tinker-OpenMM as a demonstration of the capability of Tinker-OpenMM to calculate the virial with sufficient accuracy to enable pressure control. These additions enable the further improvement of Tinker-OpenMM to include a wide range of virial-based barostat algorithms.

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Figures

Figure 1:
Figure 1:
Average density for Berendsen GPU and Berendsen CPU MD simulations on water at various pressures. Values are reported as average ± standard deviation. First 200ps of simulation time was ignored in calculation. CPU simulations were conducted for 1ns, and GPU simulations were simulated for 30ns.
Figure 2:
Figure 2:
Average density for Berendsen GPU and Monte Carlo GPU simulations on water at various pressures. Values are reported as average ±standard deviation. First 200ps of simulation time was ignored in calculation. Both series of simulations were simulated for 30ns.
See this image and copyright information in PMC

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