在Tinker-OpenMM中使用AMOEBA在GPU上基于维里的贝伦德森压力调节器
Virial Based Berendsen Barostat on GPUs using AMOEBA in Tinker-OpenMM.
作者信息
Harger Matthew, Ren Pengyu
机构信息
Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States.
出版信息
Results Chem. 2019 Jan;1. doi: 10.1016/j.rechem.2019.100004. Epub 2019 Jun 20.
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.
摘要
由于缺乏维里计算，用于GPU上的AMOEBA分子动力学的Tinker-OpenMM软件包长期以来仅限于蒙特卡罗压力调节器。在本文中，我们报告了AMOEBA力场的内维里计算。这构成了可极化内维里的首个GPU实现。随后，将Berendsen压力调节器实现到Tinker-OpenMM中，以证明Tinker-OpenMM有能力以足够的精度计算维里以实现压力控制。这些新增功能使Tinker-OpenMM能够进一步改进，以纳入各种基于维里的压力调节器算法。
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