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高性能QM/MM增强采样 用GENESIS SPDYN和QSimulate-QM进行分子动力学模拟.

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  • 1Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

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科学领域:

  • 计算化学计算化学
  • 分子动力学分子动力学
  • 生物物理学的生物物理.

背景情况:

  • 精确的分子模拟需要整合反应区域的量子力学 (QM) 和环境的分子力学 (MM).
  • 现有的QM/MM方法在计算效率和处理周期性边界条件方面面临挑战.

研究的目的:

  • 在GENESIS分子动力学计划中开发和实施一种新的QM/MM模块.
  • 提高QM/MM模拟的计算性能和适用性,特别是用于增强的采样技术.

主要方法:

  • 在GENESIS中,QSimulate-QM (电子结构) 与SPDYN (分子动力学) 的集成.
  • 使用现实空间QM计算和MM收费的粒子网格Ewald (PME) 实现周期性边界条件.
  • 优化密度功能紧固结合 (DFTB) 计算和QM/MM相互作用的多极扩展.
  • 应用增强的采样方法:通用复制品交换溶液化 (gREST),复制品交换采样 (REUS) 和路径采样.

主要成果:

  • 为QM/MM-MD模拟 (在单个节点上超过1 ns/day) 实现高性能,QM区域高达~100个原子,MM区域高达~100,000个原子.
  • 通过使用QM/MM-MD成功计算了阿拉宁二的Ramachandran图.
  • 计算了QM/MM水平上一个酶中的质子转移反应的平均力 (PMF) 的潜力.

结论:

  • 开发的QM/MM模块显著提高了分子动力学模拟的效率和能力.
  • 这种新工具可以使用先进的采样方法来研究生物系统中复杂的化学过程.
  • 方便对酶反应和分子构造进行原子级别的研究.