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快速极化水分子模型用于原子模拟。

Fast Polarizable Water Model for Atomistic Simulations.

机构信息

Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg24061, United States.

Pharmaceutical Development Department, Genentech, South San Francisco94080, United States.

出版信息

J Chem Theory Comput. 2022 Oct 11;18(10):6324-6333. doi: 10.1021/acs.jctc.2c00378. Epub 2022 Oct 3.

Abstract

Simulating water accurately has been a major challenge in atomistic simulations for decades. Inclusion of electronic polarizability effects holds considerable promise, yet existing approaches suffer from significant computational overheads compared to the widely used nonpolarizable water models. We have developed a globally optimal polarizable water model, OPC3-pol, that explicitly accounts for electronic polarizability with minimal impact on the computational efficiency. OPC3-pol reproduces five key bulk water properties at room temperature with an average relative error of 0.6%. In atomistic simulations, OPC3-pol's computational efficiency is in between that of 3- and 4-point nonpolarizable models; the model supports increased (4 fs) integration time step. OPC3-pol is tested in simulations of globular protein ubiquitin and a B-DNA dodecamer with several AMBER force fields, ff99SB, ff14SB, ff19SB, and OL15, demonstrating structure stability close to reference on multi-microsecond time scale. Simulation of an intrinsically disordered amyloid β-peptide yields an ensemble with the radius of gyration of a random coil. The proposed water model can be trivially adopted by any package that supports standard nonpolarizable force fields and water models; its intended use is in long classical atomistic simulations where water polarization effects are expected to be important.

摘要

准确模拟水一直是原子模拟几十年来的主要挑战。包含电子极化率效应具有很大的潜力,但与广泛使用的非极化水模型相比,现有方法的计算开销很大。我们开发了一种全局最优的极化水模型 OPC3-pol,它以最小的计算效率影响明确考虑了电子极化率。OPC3-pol 在室温下再现了五个关键的体相水性质,平均相对误差为 0.6%。在原子模拟中,OPC3-pol 的计算效率介于 3 点和 4 点非极化模型之间;该模型支持增加(4 fs)积分时间步长。OPC3-pol 在使用几种 AMBER 力场(ff99SB、ff14SB、ff19SB 和 OL15)的球状蛋白泛素和 B-DNA 十二聚体的模拟中进行了测试,在多微秒时间尺度上证明了接近参考的结构稳定性。对固有无序的淀粉样β肽的模拟产生了一个具有无规卷曲的回转半径的集合体。所提出的水模型可以轻松地被任何支持标准非极化力场和水模型的软件包采用;其预期用途是在需要考虑水分子极化效应的长程经典原子模拟中。

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