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For: Bashardanesh Z, van der Spoel D. Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids. J Phys Chem B 2018;122:8018-8027. [DOI: 10.1021/acs.jpcb.8b05770] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Number Cited by Other Article(s)
1
Kříž K, Schmidt L, Andersson AT, Walz MM, van der Spoel D. An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. J Chem Inf Model 2023;63:412-431. [PMID: 36630710 PMCID: PMC9875315 DOI: 10.1021/acs.jcim.2c01127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 01/12/2023]
2
Fadda E. Molecular simulations of complex carbohydrates and glycoconjugates. Curr Opin Chem Biol 2022;69:102175. [PMID: 35728307 DOI: 10.1016/j.cbpa.2022.102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
3
Franco LR, Toledo KCF, Matias TA, Benavides PA, Cezar HM, Araujo CM, Coutinho K, Araki K. Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand. Phys Chem Chem Phys 2022;24:10222-10240. [PMID: 35420602 DOI: 10.1039/d1cp03912a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
4
Qiu Y, Shan W, Zhang H. Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions. J Chem Inf Model 2021;61:3571-3582. [PMID: 34185520 DOI: 10.1021/acs.jcim.1c00339] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
5
Spoel D, Zhang J, Zhang H. Quantitative predictions from molecular simulations using explicit or implicit interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1560] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
6
Kashefolgheta S, Wang S, Acree WE, Hünenberger PH. Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies. Phys Chem Chem Phys 2021;23:13055-13074. [PMID: 34105547 PMCID: PMC8207520 DOI: 10.1039/d1cp00215e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022]
7
Jedwabny W, Dyguda-Kazimierowicz E, Pernal K, Szalewicz K, Patkowski K. Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts. J Phys Chem A 2021;125:1787-1799. [PMID: 33620223 PMCID: PMC8028329 DOI: 10.1021/acs.jpca.0c11347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/10/2021] [Indexed: 12/17/2022]
8
Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020;16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
9
Mohebifar M, Rowley CN. An efficient and accurate model for water with an improved non-bonded potential. J Chem Phys 2020;153:134105. [PMID: 33032419 DOI: 10.1063/5.0014469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
10
Kamiya N, Kayanuma M, Fujitani H, Shinoda K. A New Lipid Force Field (FUJI). J Chem Theory Comput 2020;16:3664-3676. [PMID: 32384238 DOI: 10.1021/acs.jctc.9b01195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
11
Kubincová A, Riniker S, Hünenberger PH. Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff. Phys Chem Chem Phys 2020;22:26419-26437. [DOI: 10.1039/d0cp03835k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
12
Bashardanesh Z, Elf J, Zhang H, van der Spoel D. Rotational and Translational Diffusion of Proteins as a Function of Concentration. ACS OMEGA 2019;4:20654-20664. [PMID: 31858051 PMCID: PMC6906769 DOI: 10.1021/acsomega.9b02835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 05/21/2023]
13
Oliveira Bortot L, Bashardanesh Z, van der Spoel D. Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. J Chem Inf Model 2019;60:322-331. [DOI: 10.1021/acs.jcim.9b00971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
14
van der Spoel D, Manzetti S, Zhang H, Klamt A. Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods. ACS OMEGA 2019;4:13772-13781. [PMID: 31497695 PMCID: PMC6713992 DOI: 10.1021/acsomega.9b01277] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/27/2019] [Indexed: 05/05/2023]
15
Krämer A, Pickard FC, Huang J, Venable RM, Simmonett AC, Reith D, Kirschner KN, Pastor RW, Brooks BR. Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects. J Chem Theory Comput 2019;15:3854-3867. [PMID: 31002505 DOI: 10.1021/acs.jctc.9b00016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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