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For: Bejagam KK, Singh S, An Y, Berry C, Deshmukh SA. PSO-Assisted Development of New Transferable Coarse-Grained Water Models. J Phys Chem B 2018;122:1958-1971. [DOI: 10.1021/acs.jpcb.7b10542] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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
Shi L, Wang F, Mandal T, Larson RG. Can Coarse-Grained Molecular Dynamics Simulations Predict Pharmaceutical Crystal Growth? J Chem Theory Comput 2025;21:3321-3334. [PMID: 40095948 DOI: 10.1021/acs.jctc.5c00040] [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: 03/19/2025]
2
Sose AT, Gustke T, Wang F, Anand G, Pasupuleti S, Savara A, Deshmukh SA. Evaluation of Sampling Algorithms Used for Bayesian Uncertainty Quantification of Molecular Dynamics Force Fields. J Chem Theory Comput 2024;20:5732-5742. [PMID: 38924093 PMCID: PMC11238537 DOI: 10.1021/acs.jctc.4c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
3
Stroh KS, Souza PCT, Monticelli L, Risselada HJ. CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization. J Chem Theory Comput 2023;19:8384-8400. [PMID: 37971301 PMCID: PMC10688431 DOI: 10.1021/acs.jctc.3c00637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
4
Singh SK, Sose AT, Wang F, Bejagam KK, Deshmukh SA. Data Driven Discovery of MOFs for Hydrogen Gas Adsorption. J Chem Theory Comput 2023;19:6686-6703. [PMID: 37756641 DOI: 10.1021/acs.jctc.3c00081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
5
Danielsson A, Samsonov SA, Liwo A, Sieradzan AK. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. J Chem Theory Comput 2023;19:6023-6036. [PMID: 37587433 PMCID: PMC10500997 DOI: 10.1021/acs.jctc.3c00511] [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: 05/17/2023] [Indexed: 08/18/2023]
6
Mohammadi E, Joshi SY, Deshmukh SA. Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models. Biomacromolecules 2023;24:4078-4092. [PMID: 37603467 DOI: 10.1021/acs.biomac.3c00441] [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: 08/23/2023]
7
Ma M, Song J, Dong Y, Fang W, Gao L. Structural and thermodynamic properties of bulk triglycerides and triglyceride/water mixtures reproduced using a polarizable coarse-grained model. Phys Chem Chem Phys 2023;25:22232-22243. [PMID: 37577752 DOI: 10.1039/d3cp01839c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
8
Khan P, Kaushik R, Jayaraj A. Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer-Nanoparticle Hybrid Systems. ACS OMEGA 2022;7:47567-47586. [PMID: 36591142 PMCID: PMC9798744 DOI: 10.1021/acsomega.2c06248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
9
Nguyen HTL, Huang DM. Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles. J Chem Phys 2022;156:184118. [DOI: 10.1063/5.0085006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
10
Empereur-Mot C, Capelli R, Perrone M, Caruso C, Doni G, Pavan GM. Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG. J Chem Phys 2022;156:024801. [PMID: 35032979 DOI: 10.1063/5.0079044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
11
Kubincová A, Riniker S, Hünenberger PH. Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. J Chem Phys 2021;155:094107. [PMID: 34496576 DOI: 10.1063/5.0057384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
Li M, Zhang JZH. Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipoles. Phys Chem Chem Phys 2021;23:8926-8935. [PMID: 33876052 DOI: 10.1039/d1cp00338k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
13
Song J, Wan M, Yang Y, Gao L, Fang W. Development of accurate coarse-grained force fields for weakly polar groups by an indirect parameterization strategy. Phys Chem Chem Phys 2021;23:6763-6774. [PMID: 33720253 DOI: 10.1039/d1cp00032b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
14
Wan M, Song J, Yang Y, Gao L, Fang W. Development of coarse-grained force field for alcohols: an efficient meta-multilinear interpolation parameterization algorithm. Phys Chem Chem Phys 2021;23:1956-1966. [PMID: 33464253 DOI: 10.1039/d0cp05503d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
15
Empereur-Mot C, Pesce L, Doni G, Bochicchio D, Capelli R, Perego C, Pavan GM. Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. ACS OMEGA 2020;5:32823-32843. [PMID: 33376921 PMCID: PMC7758974 DOI: 10.1021/acsomega.0c05469] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/26/2020] [Indexed: 05/23/2023]
16
Li M, Lu W, Zhang JZ. A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles. Phys Chem Chem Phys 2020;22:26289-26298. [PMID: 33174895 DOI: 10.1039/d0cp04782a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
17
Dunbar M, Keten S. Energy Renormalization for Coarse-Graining a Biomimetic Copolymer, Poly(catechol-styrene). Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
18
Joshi SY, Deshmukh SA. A review of advancements in coarse-grained molecular dynamics simulations. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1828583] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
19
Gao P, Yang X, Tartakovsky AM. Learning Coarse-Grained Potentials for Binary Fluids. J Chem Inf Model 2020;60:3731-3745. [PMID: 32668158 DOI: 10.1021/acs.jcim.0c00337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Mesoporous Mn-Doped Fe Nanoparticle-Modified Reduced Graphene Oxide for Ethyl Violet Elimination: Modeling and Optimization Using Artificial Intelligence. Processes (Basel) 2020. [DOI: 10.3390/pr8040488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
21
Wan M, Song J, Li W, Gao L, Fang W. Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm. J Comput Chem 2019;41:814-829. [DOI: 10.1002/jcc.26131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/07/2019] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
22
Bejagam KK, Singh SK, Ahn R, Deshmukh SA. Unraveling the Conformations of Backbone and Side Chains in Thermosensitive Bottlebrush Polymers. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
An Y, Singh S, Bejagam KK, Deshmukh SA. Development of an Accurate Coarse-Grained Model of Poly(acrylic acid) in Explicit Solvents. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00615] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
24
An Y, Bejagam KK, Deshmukh SA. Development of Transferable Nonbonded Interactions between Coarse-Grained Hydrocarbon and Water Models. J Phys Chem B 2019;123:909-921. [DOI: 10.1021/acs.jpcb.8b07990] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
25
Bejagam KK, An Y, Singh S, Deshmukh SA. Machine-Learning Enabled New Insights into the Coil-to-Globule Transition of Thermosensitive Polymers Using a Coarse-Grained Model. J Phys Chem Lett 2018;9:6480-6488. [PMID: 30372083 DOI: 10.1021/acs.jpclett.8b02956] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
26
Bejagam KK, Singh S, An Y, Deshmukh SA. Machine-Learned Coarse-Grained Models. J Phys Chem Lett 2018;9:4667-4672. [PMID: 30024761 DOI: 10.1021/acs.jpclett.8b01416] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
27
An Y, Bejagam KK, Deshmukh SA. Development of New Transferable Coarse-Grained Models of Hydrocarbons. J Phys Chem B 2018;122:7143-7153. [DOI: 10.1021/acs.jpcb.8b03822] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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