Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
J Chem Phys. 2017 Oct 7;147(13):134909. doi: 10.1063/1.4986194.
Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method and the force matching procedure, and find that both methodologies give similar results. The results of the FPMD simulations are compared to all-atom simulations of the same system and we find that differences between these simulations and the ones using the hybrid scheme are in a similar range as the differences obtained when using different atomistic force fields. Thus, a hybrid scheme yields qualitatively correct results in the strong non-equilibrium situation the system is experiencing in FPMD simulations.
混合模拟中，系统的一部分采用原子分辨率处理，其余部分采用粗粒化水平表示，允许快速采样，同时使用原子力场的准确性。我们应用混合方案，使用力探针分子动力学 (FPMD) 模拟研究分子复合物的机械展开和重折叠。溶剂分子的自由度采用粗粒化方式处理，而溶质保持原子分辨率。使用虚拟位点提供溶剂和溶质之间的耦合。我们测试了两种不同的常见粗粒化程序，迭代 Boltzmann 反演方法和力匹配程序，并发现这两种方法都给出了相似的结果。FPMD 模拟的结果与相同系统的全原子模拟进行了比较，我们发现这些模拟与使用混合方案之间的差异与使用不同原子力场获得的差异相似。因此，在 FPMD 模拟中系统经历的强非平衡情况下，混合方案产生定性正确的结果。
