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本文引用的文献

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How good are polarizable and flexible models for water: Insights from a many-body perspective.极化可变形水模型的性能如何:多体视角的见解
J Chem Phys. 2020 Aug 14;153(6):060901. doi: 10.1063/5.0017590.
2
Similarities and Differences between Na and K Distributions around DNA Obtained with Three Popular Water Models.三种常用水分子模型获得的 DNA 周围 Na 和 K 分布的异同。
J Chem Theory Comput. 2021 Nov 9;17(11):7246-7259. doi: 10.1021/acs.jctc.1c00332. Epub 2021 Oct 11.
3
Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.生物分子建模与模拟:蓬勃发展的多学科领域。
Annu Rev Biophys. 2021 May 6;50:267-301. doi: 10.1146/annurev-biophys-091720-102019. Epub 2021 Feb 19.
4
Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator.探究改进显式水分子模型的优化策略:基于德拜振荡器的刚性 n 点模型和极化模型。
PLoS One. 2019 Nov 14;14(11):e0224991. doi: 10.1371/journal.pone.0224991. eCollection 2019.
5
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.ff19SB:针对溶液中量子力学能量面进行训练的氨基酸特异性蛋白质骨架参数。
J Chem Theory Comput. 2020 Jan 14;16(1):528-552. doi: 10.1021/acs.jctc.9b00591. Epub 2019 Dec 3.
6
AMOEBA+ Classical Potential for Modeling Molecular Interactions.用于分子相互作用建模的AMOEBA+经典势
J Chem Theory Comput. 2019 Jul 9;15(7):4122-4139. doi: 10.1021/acs.jctc.9b00261. Epub 2019 Jun 11.
7
Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.用于生物分子模拟的极化力场:最新进展和应用。
Annu Rev Biophys. 2019 May 6;48:371-394. doi: 10.1146/annurev-biophys-070317-033349. Epub 2019 Mar 27.
8
The combined force field-sampling problem in simulations of disordered amyloid-β peptides.无序态淀粉样-β肽模拟中的联合力场采样问题。
J Chem Phys. 2019 Mar 14;150(10):104108. doi: 10.1063/1.5078615.
9
General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins.通用水模型可改善对无序蛋白的原子模拟。
J Chem Theory Comput. 2019 Apr 9;15(4):2620-2634. doi: 10.1021/acs.jctc.8b01123. Epub 2019 Mar 26.
10
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.使用 OpenMM 在 GPU 上的 Drude 极化力场进行分子动力学模拟:实现、验证和基准测试。
J Comput Chem. 2018 Aug 5;39(21):1682-1689. doi: 10.1002/jcc.25339. Epub 2018 May 4.

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.

DOI:10.1021/acs.jctc.2c00378
PMID:36190318
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10313234/
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。