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For: Han Y, Dama JF, Voth GA. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J Chem Phys 2018;149:044104. [DOI: 10.1063/1.5039738] [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: 01/24/2023]  Open
Number Cited by Other Article(s)
1
Klippenstein V, Wolf N, van der Vegt NFA. A Gauss-Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations. J Chem Phys 2024;160:204115. [PMID: 38804493 DOI: 10.1063/5.0203832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]  Open
2
Zhang XZ, Shi R, Lu ZY, Qian HJ. Chemically Specific Systematic Coarse-Grained Polymer Model with Both Consistently Structural and Dynamical Properties. JACS AU 2024;4:1018-1030. [PMID: 38559727 PMCID: PMC10976574 DOI: 10.1021/jacsau.3c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
3
Izvekov S, Kroonblawd MP, Larentzos JP, Brennan JK, Rice BM. Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB). J Phys Chem B 2024. [PMID: 38489758 DOI: 10.1021/acs.jpcb.3c07078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
4
Palma Banos M, Popov AV, Hernandez R. Representability and Dynamical Consistency in Coarse-Grained Models. J Phys Chem B 2024;128:1506-1514. [PMID: 38315661 DOI: 10.1021/acs.jpcb.3c08054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
5
Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024;128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [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: 02/07/2024]
6
Sokhan VP, Seaton MA, Todorov IT. Phase behaviour of coarse-grained fluids. SOFT MATTER 2023. [PMID: 37470164 DOI: 10.1039/d3sm00835e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
7
Izvekov S, Rice BM. Hierarchical Machine Learning of Low-Resolution Coarse-Grained Free Energy Potentials. J Chem Theory Comput 2023. [PMID: 37256918 DOI: 10.1021/acs.jctc.3c00128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
8
Jin J, Voth GA. Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces. J Phys Chem Lett 2023;14:1354-1362. [PMID: 36728761 PMCID: PMC9940719 DOI: 10.1021/acs.jpclett.2c03844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
9
Klippenstein V, van der Vegt NFA. Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics. J Chem Theory Comput 2023;19:1099-1110. [PMID: 36745567 PMCID: PMC9979609 DOI: 10.1021/acs.jctc.2c00871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
10
Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J Chem Theory Comput 2022;18:5759-5791. [PMID: 36070494 PMCID: PMC9558379 DOI: 10.1021/acs.jctc.2c00643] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/14/2023]
11
Luo S, Thachuk M. Conservative Potentials for a Lattice-Mapped, Coarse-Grain Scheme with Fuzzy Switching Functions. J Phys Chem A 2022;126:4517-4527. [PMID: 35767684 DOI: 10.1021/acs.jpca.2c01256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
12
Luo S, Thachuk M. Conservative Potentials for a Lattice-Mapped Coarse-Grained Scheme. J Phys Chem A 2021;125:6486-6497. [PMID: 34264666 DOI: 10.1021/acs.jpca.1c02000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Klippenstein V, Tripathy M, Jung G, Schmid F, van der Vegt NFA. Introducing Memory in Coarse-Grained Molecular Simulations. J Phys Chem B 2021;125:4931-4954. [PMID: 33982567 PMCID: PMC8154603 DOI: 10.1021/acs.jpcb.1c01120] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
14
Han Y, Jin J, Voth GA. Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining. J Chem Phys 2021;154:084122. [PMID: 33639745 DOI: 10.1063/5.0035184] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
15
Jin J, Han Y, Pak AJ, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model. J Chem Phys 2021;154:044104. [PMID: 33514116 PMCID: PMC7826168 DOI: 10.1063/5.0026651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022]  Open
16
Pireddu G, Pazzona FG, Demontis P, Załuska-Kotur MA. Scaling-Up Simulations of Diffusion in Microporous Materials. J Chem Theory Comput 2019;15:6931-6943. [PMID: 31604017 DOI: 10.1021/acs.jctc.9b00801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Wang S, Li Z, Pan W. Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism. SOFT MATTER 2019;15:7567-7582. [PMID: 31436282 DOI: 10.1039/c9sm01211g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
18
Durumeric AEP, Voth GA. Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining. J Chem Phys 2019;151:124110. [PMID: 31575201 DOI: 10.1063/1.5097559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
19
Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. COMPUTATION 2019. [DOI: 10.3390/computation7030042] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
20
Zavadlav J, Marrink SJ, Praprotnik M. SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 2019;9:20180075. [PMID: 31065343 PMCID: PMC6501350 DOI: 10.1098/rsfs.2018.0075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/11/2022]  Open
21
Rosenberger D, van der Vegt NFA. Relative entropy indicates an ideal concentration for structure-based coarse graining of binary mixtures. Phys Rev E 2019;99:053308. [PMID: 31212527 DOI: 10.1103/physreve.99.053308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 06/09/2023]
22
Lynn H, Thachuk M. Equations of motion for position-dependent coarse-grain mappings obtained with Mori-Zwanzig theory. J Chem Phys 2019;150:024108. [DOI: 10.1063/1.5058061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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