Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU
Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU
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DOI：
10.1016/j.jcp.2022.111673
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发表时间：
2022-10-18
影响因子：
4.1
通讯作者：
Li，Bo
中科院分区：
文献类型：
--
作者：
Liu，Shuang;Zhang，Zirui;Li，Bo
粗粒度建模和高效的计算机模拟是研究具有多自由度和多时空尺度的复杂分子过程的关键。生物分子溶剂化的变分隐溶剂模型（VISM）就是这样一个建模框架，它的初步成功已经得到了一致的证明。在VISM中，溶质-溶剂界面的有效自由能泛函被最小化，并且表面能是自由能的关键组成部分。在这项工作中，我们扩展VISM包括溶质的机械相互作用，并开发快速算法和GPU实现的扩展变分显式溶质隐式溶剂（VESIS）分子模拟，以确定潜在的分子平衡构象。我们采用了一种快速的二进制水平集方法最小化溶质-溶剂界面的溶剂化自由能，并构建了一个自适应迁移率梯度下降法溶质原子优化。我们还实现了我们的方法上集成的GPU。数值试验和几个分子系统的应用验证了我们的方法和算法的准确性，稳定性和效率。结果发现，我们的新方法和GPU实现提高了分子模拟的效率显着超过CPU实现。我们的快速计算技术可能使我们能够模拟非常大的系统，如蛋白质-蛋白质相互作用和膜动力学，其中显式溶剂全原子分子动力学模拟可能非常昂贵。
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular solvation is such a modeling framework, and its initial success has been demonstrated consistently. In VISM, an effective free-energy functional of solute-solvent interfaces is minimized, and the surface energy is a key component of the free energy. In this work, we extend VISM to include the solute mechanical interactions, and develop fast algorithms and GPU implementation for the extended variational explicit-solute implicit-solvent (VESIS) molecular simulations to determine the underlying molecular equilibrium conformations. We employ a fast binary level-set method for minimizing the solvation free energy of solute-solvent interfaces and construct an adaptive–mobility gradient descent method for solute atomic optimization. We also implement our methods on the integrated GPU. Numerical tests and applications to several molecular systems verify the accuracy, stability, and efficiency of our methods and algorithms. It is found that our new methods and GPU implementation improve the efficiency of the molecular simulation significantly over the CPU implementation. Our fast computational techniques may enable us to simulate very large systems such as protein-protein interactions and membrane dynamics for which explicit-solvent all-atom molecular dynamics simulations can be very expensive.