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For: Zhu Q, Wu Y, Zhao S, Cieplak P, Duan Y, Luo R. Streamlining and Optimizing Strategies of Electrostatic Parameterization. J Chem Theory Comput 2023;19:6353-6365. [PMID: 37676646 PMCID: PMC10530599 DOI: 10.1021/acs.jctc.3c00659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Number Cited by Other Article(s)
1
Lapsien M, Bonus M, Gahan L, Raguin A, Gohlke H. PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges. J Chem Inf Model 2025;65:4251-4256. [PMID: 40285710 DOI: 10.1021/acs.jcim.5c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2025]
2
Huang Z, Wu X, Luo R. Isotropic Periodic Sum for Polarizable Gaussian Multipole Model. J Chem Theory Comput 2025;21:4040-4050. [PMID: 40194962 DOI: 10.1021/acs.jctc.5c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
3
Wu Y, Zhu Q, Huang Z, Cieplak P, Duan Y, Luo R. Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization. J Chem Theory Comput 2025;21:3563-3575. [PMID: 40108759 DOI: 10.1021/acs.jctc.5c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2025]
4
Duan Y, Wang J, Cieplak P, Luo R. Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials. J Chem Inf Model 2025;65:1428-1440. [PMID: 39865620 PMCID: PMC11815842 DOI: 10.1021/acs.jcim.4c02175] [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: 11/27/2024] [Revised: 01/11/2025] [Accepted: 01/14/2025] [Indexed: 01/28/2025]
5
Huang Z, Wu Y, Duan Y, Luo R. Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations. J Chem Theory Comput 2025;21:847-858. [PMID: 39772516 PMCID: PMC11854381 DOI: 10.1021/acs.jctc.4c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
6
Duan Y, Niu T, Wang J, Cieplak P, Luo R. PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents. J Chem Theory Comput 2024;20:2820-2829. [PMID: 38502776 PMCID: PMC11008095 DOI: 10.1021/acs.jctc.4c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024]
7
Zhao S, Cieplak P, Duan Y, Luo R. Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. J Chem Theory Comput 2024;20:2098-2110. [PMID: 38394331 PMCID: PMC11060985 DOI: 10.1021/acs.jctc.3c01347] [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: 02/25/2024]
8
Case D, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O’Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. AmberTools. J Chem Inf Model 2023;63:6183-6191. [PMID: 37805934 PMCID: PMC10598796 DOI: 10.1021/acs.jcim.3c01153] [Citation(s) in RCA: 573] [Impact Index Per Article: 286.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/10/2023]
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