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For: Pan X, Van R, Epifanovsky E, Liu J, Pu J, Nam K, Shao Y. Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian. J Phys Chem B 2022;126:10.1021/acs.jpcb.2c02262. [PMID: 35653199 PMCID: PMC9715852 DOI: 10.1021/acs.jpcb.2c02262] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Paz H, Beck S, Lee R, Ho J, Yu H. The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems. J Comput Chem 2025;46:e70109. [PMID: 40251879 PMCID: PMC12008714 DOI: 10.1002/jcc.70109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 03/19/2025] [Accepted: 04/05/2025] [Indexed: 04/21/2025]
2
Bonfrate S, Park W, Trejo‐Zamora D, Ferré N, Ho Choi C, Huix‐Rotllant M. Assessment of Free Energies From Electrostatic Embedding Density Functional Tight Binding-Based/Molecular Mechanics in Periodic Boundary Conditions. J Comput Chem 2025;46:e70107. [PMID: 40260846 PMCID: PMC12012883 DOI: 10.1002/jcc.70107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 03/26/2025] [Accepted: 04/02/2025] [Indexed: 04/24/2025]
3
Yagi K, Gunst K, Shiozaki T, Sugita Y. High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM. J Chem Theory Comput 2025;21:4016-4029. [PMID: 40174884 PMCID: PMC12020374 DOI: 10.1021/acs.jctc.5c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 03/10/2025] [Accepted: 03/12/2025] [Indexed: 04/04/2025]
4
Arattu Thodika A, Pan X, Shao Y, Nam K. Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions. J Chem Theory Comput 2025;21:817-832. [PMID: 39815393 PMCID: PMC11781312 DOI: 10.1021/acs.jctc.4c01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/30/2024] [Accepted: 01/03/2025] [Indexed: 01/18/2025]
5
Van R, Pan X, Rostami S, Liu J, Agarwal PK, Brooks B, Rajan R, Shao Y. Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation. Biochemistry 2025;64:289-299. [PMID: 39680038 PMCID: PMC12005057 DOI: 10.1021/acs.biochem.4c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
6
Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024;128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
7
Zheng J, Frisch MJ. Multiple-time scale integration method based on an interpolated potential energy surface for ab initio path integral molecular dynamics. J Chem Phys 2024;160:144111. [PMID: 38597307 DOI: 10.1063/5.0196634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]  Open
8
Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024;9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
9
McFarlane NR, Harvey JN. Exploration of biochemical reactivity with a QM/MM growing string method. Phys Chem Chem Phys 2024;26:5999-6007. [PMID: 38293892 DOI: 10.1039/d3cp05772k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
10
Yuan Y, Cui Q. Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling. J Chem Theory Comput 2023;19:5394-5406. [PMID: 37527495 PMCID: PMC10810721 DOI: 10.1021/acs.jctc.3c00591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
11
Snyder R, Kim B, Pan X, Shao Y, Pu J. Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation. J Chem Phys 2023;159:054107. [PMID: 37530109 PMCID: PMC10400118 DOI: 10.1063/5.0156327] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023]  Open
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