1
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Lesniewski MC, Noid WG. Insight into the Density-Dependence of Pair Potentials for Predictive Coarse-Grained Models. J Phys Chem B 2024; 128:1298-1316. [PMID: 38271676 DOI: 10.1021/acs.jpcb.3c06890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigate the temperature- and density-dependence of effective pair potentials for 1-site coarse-grained (CG) models of two industrial solvents, 1,4-dioxane and tetrahydrofuran. We observe that the calculated pair potentials are much more sensitive to density than to temperature. The generalized-Yvon-Born-Green framework reveals that this striking density-dependence reflects corresponding variations in the many-body correlations that determine the environment-mediated indirect contribution to the pair mean force. Moreover, we demonstrate, perhaps surprisingly, that this density-dependence is not important for accurately modeling the intermolecular structure. Accordingly, we adopt a density-independent interaction potential and transfer the density-dependence of the calculated pair potentials into a configuration-independent volume potential. Furthermore, we develop a single global potential that accurately models the intermolecular structure and pressure-volume equation of state across a very wide range of liquid state points. Consequently, this work provides fundamental insight into the density-dependence of effective pair potentials and also provides a significant step toward developing predictive CG models for efficiently modeling industrial solvents.
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Affiliation(s)
- Maria C Lesniewski
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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2
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Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
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3
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Development of coarse-grained force field to investigate sodium-ion transport mechanisms in cyanoborate-based ionic liquid. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Sherck N, Shen K, Nguyen M, Yoo B, Köhler S, Speros JC, Delaney KT, Shell MS, Fredrickson GH. Molecularly Informed Field Theories from Bottom-up Coarse-Graining. ACS Macro Lett 2021; 10:576-583. [PMID: 35570772 DOI: 10.1021/acsmacrolett.1c00013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polymer formulations possessing mesostructures or phase coexistence are challenging to simulate using atomistic particle-explicit approaches due to the disparate time and length scales, while the predictive capability of field-based simulations is hampered by the need to specify interactions at a coarser scale (e.g., χ-parameters). To overcome the weaknesses of both, we introduce a bottom-up coarse-graining methodology that leverages all-atom molecular dynamics to molecularly inform coarser field-theoretic models. Specifically, we use relative-entropy coarse-graining to parametrize particle models that are directly and analytically transformable into statistical field theories. We demonstrate the predictive capability of this approach by reproducing experimental aqueous poly(ethylene oxide) (PEO) cloud-point curves with no parameters fit to experimental data. This synergistic approach to multiscale polymer simulations opens the door to de novo exploration of phase behavior across a wide variety of polymer solutions and melt formulations.
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Affiliation(s)
- Nicholas Sherck
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kevin Shen
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - My Nguyen
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Brian Yoo
- BASF Corporation, Tarrytown, New York 10591, United States
| | | | - Joshua C. Speros
- California Research Alliance (CARA) by BASF, Berkeley, California 94720, United States
| | - Kris T. Delaney
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - M. Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Glenn H. Fredrickson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
- Department of Materials, University of California, Santa Barbara, California 93106, United States
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5
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Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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6
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Wen C, Odle R, Cheng S. Coarse-Grained Molecular Dynamics Modeling of a Branched Polyetherimide. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c01440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Chengyuan Wen
- Department of Physics, Center for Soft Matter and Biological Physics, and Macromolecules Innovation Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Roy Odle
- SABIC, 1 Lexan Lane, Mt. Vernon, Indiana 47620, United States
| | - Shengfeng Cheng
- Department of Physics, Center for Soft Matter and Biological Physics, and Macromolecules Innovation Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
- Department of Mechanical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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7
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Shen K, Sherck N, Nguyen M, Yoo B, Köhler S, Speros J, Delaney KT, Fredrickson GH, Shell MS. Learning composition-transferable coarse-grained models: Designing external potential ensembles to maximize thermodynamic information. J Chem Phys 2020; 153:154116. [DOI: 10.1063/5.0022808] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Kevin Shen
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
| | - Nicholas Sherck
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - My Nguyen
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Brian Yoo
- BASF Corporation, Tarrytown, New York 10591, USA
| | | | - Joshua Speros
- California Research Alliance (CARA) by BASF, Berkeley, California 94720, USA
| | - Kris T. Delaney
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
| | - Glenn H. Fredrickson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
- Department of Materials Engineering, University of California, Santa Barbara, California 93106, USA
| | - M. Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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8
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Eriksen JJ, Anderson TA, Deustua JE, Ghanem K, Hait D, Hoffmann MR, Lee S, Levine DS, Magoulas I, Shen J, Tubman NM, Whaley KB, Xu E, Yao Y, Zhang N, Alavi A, Chan GKL, Head-Gordon M, Liu W, Piecuch P, Sharma S, Ten-No SL, Umrigar CJ, Gauss J. The Ground State Electronic Energy of Benzene. J Phys Chem Lett 2020; 11:8922-8929. [PMID: 33022176 DOI: 10.1021/acs.jpclett.0c02621] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report on the findings of a blind challenge devoted to determining the frozen-core, full configuration interaction (FCI) ground-state energy of the benzene molecule in a standard correlation-consistent basis set of double-ζ quality. As a broad international endeavor, our suite of wave function-based correlation methods collectively represents a diverse view of the high-accuracy repertoire offered by modern electronic structure theory. In our assessment, the evaluated high-level methods are all found to qualitatively agree on a final correlation energy, with most methods yielding an estimate of the FCI value around -863 mEH. However, we find the root-mean-square deviation of the energies from the studied methods to be considerable (1.3 mEH), which in light of the acclaimed performance of each of the methods for smaller molecular systems clearly displays the challenges faced in extending reliable, near-exact correlation methods to larger systems. While the discrepancies exposed by our study thus emphasize the fact that the current state-of-the-art approaches leave room for improvement, we still expect the present assessment to provide a valuable community resource for benchmark and calibration purposes going forward.
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Affiliation(s)
- Janus J Eriksen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Tyler A Anderson
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, United States
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Khaldoon Ghanem
- Max-Planck-Institut für Festkörperforschung, 70569 Stuttgart, Germany
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Mark R Hoffmann
- Chemistry Department, University of North Dakota, Grand Forks, North Dakota 58202-9024, United States
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Norm M Tubman
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - K Birgitta Whaley
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Enhua Xu
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Yuan Yao
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, United States
| | - Ning Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ali Alavi
- Max-Planck-Institut für Festkörperforschung, 70569 Stuttgart, Germany
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Sandeep Sharma
- Department of Chemistry, The University of Colorado at Boulder, Boulder, Colorado 80302, United States
| | - Seiichiro L Ten-No
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - C J Umrigar
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, United States
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz,Duesbergweg 10-14, 55128 Mainz, Germany
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9
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Imamura K, Yamamoto T, Sato H. Coarse-grained modeling of nanocube self-assembly system and transition network analyses. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Li C, Qin Z, Han W. Bottom-up derived flexible water model with dipole and quadrupole moments for coarse-grained molecular simulations. Phys Chem Chem Phys 2020; 22:27394-27412. [DOI: 10.1039/d0cp04185h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bottom-up CG water model is developed to capture the electrostatic multipoles, structural correlation and thermodynamics of water.
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Affiliation(s)
- Chen Li
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zhongyuan Qin
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Wei Han
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
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11
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Kumar A, Mahato J, Dixit M, Patwari GN. Progressive Hydrophobicity of Fluorobenzenes. J Phys Chem B 2019; 123:10083-10088. [PMID: 31661279 DOI: 10.1021/acs.jpcb.9b08057] [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]
Abstract
The potentials of mean force for the dimers of fluorobenzenes sample both π-stacked and T-shaped structures for partially fluorinated benzenes, namely, 1,4-difluorobenzene, 1,3,5-trifluorobenzene, and 1,2,4,5-tetrafluorobenzene, and sample only the T-shaped structures for benzene and hexafluorobenzene. While the free energy for the dimerization in water is very weakly dependent on the number of fluorine atoms, the formation of π-stacked structures is entropy-driven and the T-shaped structures appear due to an enthalpic minimum. Interestingly, the solvation behavior suggests that the accumulation of water around the contact and solvent-separated pairs decreases with the increase in the number of fluorine atoms, which signifies progressive hydrophobicity of fluorobenzenes.
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Affiliation(s)
- Anuj Kumar
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India.,Prithwi Chand Vigyan College, Jai Prakash Vishwavidyalaya , Chapra , Saran, Bihar 841301 , India
| | - Jaladhar Mahato
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
| | - Mayank Dixit
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
| | - G Naresh Patwari
- Department of Chemistry , Indian Institute of Technology Bombay , Powai, Mumbai 400076 India
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12
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Kato T, Schäfer K, Jaschonek S, Gauss J, Diezemann G. Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations. J Chem Phys 2019; 151:045102. [DOI: 10.1063/1.5111717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Takashi Kato
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Ken Schäfer
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Stefan Jaschonek
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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13
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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]
Abstract
Many methodological approaches have been proposed to improve systematic or bottom-up coarse-graining techniques to enhance the representability and transferability of the derived interaction potentials. Transferability describes the ability of a coarse-grained (CG) model to be predictive, i.e., to describe a system at state points different from those chosen for parametrization. Whereas the representability characterizes the accuracy of a CG model to reproduce target properties of the underlying reference or fine-grained model at a given state point. In this article, we shift the focus away from methodological aspects and rather raise the question whether we can overcome the disadvantages of a given method in terms of representability and transferability by systematically selecting the state point at which the CG model gets parametrized. We answer this question by applying the inverse Monte Carlo (IMC) approach-a structure-based coarse-graining method-to derive effective interactions for binary mixtures of simple Lennard-Jones (LJ) particles, which are different in size. For such simple systems we indeed can identify a concentration where the derived potentials show the best performance in terms of structural representability and transferability. This specific concentration is identified by computing the relative entropy which quantifies the information loss between different IMC models and the reference LJ model at varying mixture compositions. Further, we show that an IMC model for mixtures of n-hexane and n-perfluorohexane shows the same trend in transferability as the IMC models for the LJ system. All derived models are more transferable in the direction of increasing concentration of the larger-sized compound.
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Affiliation(s)
- David Rosenberger
- Eduard Zintl Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Darmstadt, 64287, Germany
| | - Nico F A van der Vegt
- Eduard Zintl Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Darmstadt, 64287, Germany
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14
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Deichmann G, van der Vegt NFA. Conditional Reversible Work Coarse-Grained Models with Explicit Electrostatics—An Application to Butylmethylimidazolium Ionic Liquids. J Chem Theory Comput 2019; 15:1187-1198. [DOI: 10.1021/acs.jctc.8b00881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gregor Deichmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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15
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Junxi L, Yingxue W, Li L. Effects of substitutions in the equatorial position on the stabilities of pentacoordinated silicon anions of ClSi abc
OCl −
( a
, b
, c
= H, F, Cl) from theoretical investigation. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201700421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Liang Junxi
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering; Northwest Minzu University; Lanzhou Gansu China
| | - Wang Yingxue
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering; Northwest Minzu University; Lanzhou Gansu China
| | - Liu Li
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering; Northwest Minzu University; Lanzhou Gansu China
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16
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Sanyal T, Shell MS. Transferable Coarse-Grained Models of Liquid-Liquid Equilibrium Using Local Density Potentials Optimized with the Relative Entropy. J Phys Chem B 2018; 122:5678-5693. [PMID: 29466859 DOI: 10.1021/acs.jpcb.7b12446] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bottom-up coarse-grained (CG) models are now regularly pursued to enable large length and time scale molecular simulations of complex, often macromolecular systems. However, predicting fluid phase equilibria using such models remains fundamentally challenging. A major problem stems from the typically low transferability of CG models beyond the densities and/or compositions at which they are parametrized, which is necessary if they are to describe distinct structural and thermodynamic properties unique to each phase. CG model transferability is compounded by the representation of the inherently multibody coarse interactions using pair potentials that neglect higher order effects. Here, we propose to construct transferable single site CG models of liquid mixtures by supplementing traditional CG pair interactions with local density potentials, which constitute a computationally inexpensive mean-field approach to describe many-body effects, in that site energies are modulated by the local solution environment. To illustrate the approach, we use intra- and interspecies local density potentials to develop CG models of benzene-water solutions that show impressive transferability in structural metrics (pair correlation functions, density profiles) throughout composition space, in contrast to pair-only CG representations. While further refinement may be necessary to represent more complex thermodynamic properties, like the liquid-liquid interfacial tension, the generality and improvement offered by the local density approach are highly encouraging for enabling complex phase equilibrium modeling using CG models.
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Affiliation(s)
- Tanmoy Sanyal
- Department of Chemical Engineering , University of California, Santa Barbara , Santa Barbara , California , United States
| | - M Scott Shell
- Department of Chemical Engineering , University of California, Santa Barbara , Santa Barbara , California , United States
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17
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Rosenberger D, van der Vegt NFA. Addressing the temperature transferability of structure based coarse graining models. Phys Chem Chem Phys 2018; 20:6617-6628. [DOI: 10.1039/c7cp08246k] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a novel idea to improve the temperature transferability of structure based coarse graining models.
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Affiliation(s)
- David Rosenberger
- Technische Universität Darmstadt, Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Darmstadt
- Germany
| | - Nico F. A. van der Vegt
- Technische Universität Darmstadt, Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Darmstadt
- Germany
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18
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Deichmann G, van der Vegt NFA. Conditional Reversible Work Coarse-Grained Models of Molecular Liquids with Coulomb Electrostatics – A Proof of Concept Study on Weakly Polar Organic Molecules. J Chem Theory Comput 2017; 13:6158-6166. [DOI: 10.1021/acs.jctc.7b00611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gregor Deichmann
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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19
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Abstract
In recent years, it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely, the memory kernel, from equilibrium all-atom simulations. In this article, we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed noniterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and discretization effects. Furthermore, we also propose a new numerical integrator for generalized Langevin equations that is significantly more accurate than the more commonly used generalization of the velocity Verlet integrator. We demonstrate the performance of the above-described methods using the example of backflow-induced memory in the Brownian diffusion of a single colloid. For this system, we are able to reconstruct realistic coarse-grained dynamics with time steps about 200 times larger than those used in the original molecular dynamics simulations.
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Affiliation(s)
- Gerhard Jung
- Institut für Physik, ‡Graduate School of Excellence Materials Science in Mainz, §Institut für Mathematik, Johannes Gutenberg-Universität Mainz , Staudingerweg 9, 55128 Mainz, Germany
| | - Martin Hanke
- Institut für Physik, ‡Graduate School of Excellence Materials Science in Mainz, §Institut für Mathematik, Johannes Gutenberg-Universität Mainz , Staudingerweg 9, 55128 Mainz, Germany
| | - Friederike Schmid
- Institut für Physik, ‡Graduate School of Excellence Materials Science in Mainz, §Institut für Mathematik, Johannes Gutenberg-Universität Mainz , Staudingerweg 9, 55128 Mainz, Germany
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20
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Sanyal T, Shell MS. Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation. J Chem Phys 2017; 145:034109. [PMID: 27448876 DOI: 10.1063/1.4958629] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.
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Affiliation(s)
- Tanmoy Sanyal
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
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21
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Zhang C, Bell D, Harger M, Ren P. Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases. J Chem Theory Comput 2017; 13:666-678. [PMID: 28030769 PMCID: PMC5312700 DOI: 10.1021/acs.jctc.6b00918] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Aromatic molecules with π electrons
are commonly involved
in chemical and biological recognitions. For example, nucleobases
play central roles in DNA/RNA structure and their interactions with
proteins. The delocalization of the π electrons is responsible
for the high polarizability of aromatic molecules. In this work, the
AMOEBA force field has been developed and applied to 5 regular nucleobases
and 12 aromatic molecules. The permanent electrostatic energy is expressed
as atomic multipole interactions between atom pairs, and many-body
polarization is accounted for by mutually induced atomic dipoles.
We have systematically investigated aromatic ring stacking and aromatic-water
interactions for nucleobases and aromatic molecules, as well as base–base
hydrogen-bonding pair interactions, all at various distances and orientations.
van der Waals parameters were determined by comparison to the quantum
mechanical interaction energy of these dimers and fine-tuned using
condensed phase simulation. By comparing to quantum mechanical calculations,
we show that the resulting classical potential is able to accurately
describe molecular polarizability, molecular vibrational frequency,
and dimer interaction energy of these aromatic systems. Condensed
phase properties, including hydration free energy, liquid density,
and heat of vaporization, are also in good overall agreement with
experimental values. The structures of benzene liquid phase and benzene-water
solution were also investigated by simulation and compared with experimental
and PDB structure derived statistical results.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - David Bell
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
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22
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Cao F, Deetz JD, Sun H. Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide. J Chem Inf Model 2017; 57:50-59. [DOI: 10.1021/acs.jcim.6b00685] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fenglei Cao
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joshua D. Deetz
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
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23
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Gooneie A, Schuschnigg S, Holzer C. A Review of Multiscale Computational Methods in Polymeric Materials. Polymers (Basel) 2017; 9:E16. [PMID: 30970697 PMCID: PMC6432151 DOI: 10.3390/polym9010016] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research.
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Affiliation(s)
- Ali Gooneie
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Stephan Schuschnigg
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Clemens Holzer
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
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24
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Dallavalle M, van der Vegt NFA. Evaluation of mapping schemes for systematic coarse graining of higher alkanes. Phys Chem Chem Phys 2017; 19:23034-23042. [DOI: 10.1039/c7cp03926c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different levels of coarse-graining are introduced to study the thermodynamic and structural properties of higher alkanes.
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Affiliation(s)
- Marco Dallavalle
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Center of Smart Interfaces
- Technische Universität Darmstadt
- Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Center of Smart Interfaces
- Technische Universität Darmstadt
- Germany
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25
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Zhang R, van der Vegt NFA. Study of Hydrophobic Clustering in Partially Sulfonated Polystyrene Solutions with a Systematic Coarse-Grained Model. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ran Zhang
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, D-64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, D-64287 Darmstadt, Germany
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26
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Affiliation(s)
- M. Scott Shell
- Department of Chemical Engineering; University of California Santa Barbara; Santa Barbara CA USA
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27
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Foley TT, Shell MS, Noid WG. The impact of resolution upon entropy and information in coarse-grained models. J Chem Phys 2016; 143:243104. [PMID: 26723589 DOI: 10.1063/1.4929836] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, SW, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into SW. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, -TSW is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.
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Affiliation(s)
- Thomas T Foley
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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28
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Liang L, Wang LW, Shen JW. The self-assembly mechanism of tetra-peptides from the motif of β-amyloid peptides: a combined coarse-grained and all-atom molecular dynamics simulation. RSC Adv 2016. [DOI: 10.1039/c6ra18204f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the self-assembly mechanisms of tetra-peptides from Aβ-peptides into different nanostructures.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering
- Hangzhou Dianzi University
- Hangzhou
- People’s Republic of China
| | - Li-Wei Wang
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People’s Republic of China
| | - Jia-Wei Shen
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016
- People’s Republic of China
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29
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Szklarczyk OM, Bieler NS, Hünenberger PH, van Gunsteren WF. Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:5447-63. [PMID: 26574333 DOI: 10.1021/acs.jctc.5b00406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An algorithm is proposed for performing molecular dynamics (MD) simulations of a biomolecular solute represented at atomistic resolution surrounded by a surface layer of atomistic fine-grained (FG) solvent molecules within a bulk represented by coarse-grained (CG) solvent beads. The method, called flexible boundaries for multiresolution solvation (FBMS), is based on: (i) a three-region layering of the solvent around the solute, involving an FG layer surrounded by a mixed FG-CG buffer layer, itself surrounded by a bulk CG region; (ii) a definition of the layer boundary that relies on an effective distance to the solute surface and is thus adapted to the shape of the solute as well as adjusts to its conformational changes. The effective surface distance is defined by inverse-nth power averaging over the distances to all non-hydrogen solute atoms, and the layering is enforced by means of half-harmonic distance restraints, attractive for the FG molecules and repulsive for the CG beads. A restraint-free region at intermediate distances enables the formation of the buffer layer, where the FG and CG solvents can mix freely. The algorithm is tested and validated using the GROMOS force field and the associated FG (SPC) and CG (polarizable CGW) water models. The test systems include pure-water systems, where one FG molecule plays the role of a solute, and a deca-alanine peptide with two widely different solute shapes considered, α-helical and fully extended. In particular, as the peptide unfolds, the number of FG molecules required to fill its close-range solvation layer increases, with the additional molecules being provided by the buffer layer. Further validation involves simulations of four proteins in multiresolution FG/CG mixtures. The resulting structural, energetic, and solvation properties are found to be similar to those observed in corresponding pure FG simulations.
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Affiliation(s)
- Oliwia M Szklarczyk
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
| | - Noah S Bieler
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology ETH , 8093 Zürich, Switzerland
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30
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Vafaei S, Tomberli B, Gray CG. McMillan-Mayer theory of solutions revisited: simplifications and extensions. J Chem Phys 2015; 141:154501. [PMID: 25338903 DOI: 10.1063/1.4897980] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
McMillan and Mayer (MM) proved two remarkable theorems in their paper on the equilibrium statistical mechanics of liquid solutions. They first showed that the grand canonical partition function for a solution can be reduced to one with an effectively solute-only form, by integrating out the solvent degrees of freedom. The total effective solute potential in the effective solute grand partition function can be decomposed into components which are potentials of mean force for isolated groups of one, two, three, etc., solute molecules. Second, from the first result, now assuming low solute concentration, MM derived an expansion for the osmotic pressure in powers of the solute concentration, in complete analogy with the virial expansion of gas pressure in powers of the density at low density. The molecular expressions found for the osmotic virial coefficients have exactly the same form as the corresponding gas virial coefficients, with potentials of mean force replacing vacuum potentials. In this paper, we restrict ourselves to binary liquid solutions with solute species A and solvent species B and do three things: (a) By working with a semi-grand canonical ensemble (grand with respect to solvent only) instead of the grand canonical ensemble used by MM, and avoiding graphical methods, we have greatly simplified the derivation of the first MM result, (b) by using a simple nongraphical method developed by van Kampen for gases, we have greatly simplified the derivation of the second MM result, i.e., the osmotic pressure virial expansion; as a by-product, we show the precise relation between MM theory and Widom potential distribution theory, and (c) we have extended MM theory by deriving virial expansions for other solution properties such as the enthalpy of mixing. The latter expansion is proving useful in analyzing ongoing isothermal titration calorimetry experiments with which we are involved. For the enthalpy virial expansion, we have also changed independent variables from semi-grand canonical, i.e., fixed {N(A), μ(B), V, T}, to those relevant to the experiment, i.e., fixed {N(A), N(B), p, T}, where μ denotes chemical potential, N the number of molecules, V the volume, p the pressure, and T the temperature.
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Affiliation(s)
- Shaghayegh Vafaei
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Bruno Tomberli
- Department of Physics, Capilano University, Vancouver, British Columbia V7J3H5, Canada
| | - C G Gray
- Department of Physics, University of Guelph, Guelph, Ontario N1G2W1, Canada
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31
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Cao F, Sun H. Transferability and Nonbond Functional Form of Coarse Grained Force Field – Tested on Linear Alkanes. J Chem Theory Comput 2015; 11:4760-9. [DOI: 10.1021/acs.jctc.5b00573] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fenglei Cao
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
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32
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Gopal SM, Kuhn AB, Schäfer LV. Systematic evaluation of bundled SPC water for biomolecular simulations. Phys Chem Chem Phys 2015; 17:8393-406. [DOI: 10.1039/c4cp04784b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
How accurate is bundled SPC water as inner shell solvent for hybrid all-atom/coarse-grained simulations?
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Affiliation(s)
| | | | - Lars V. Schäfer
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- Germany
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33
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34
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Mirzoev A, Lyubartsev AP. Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids. J Comput Chem 2014; 35:1208-18. [DOI: 10.1002/jcc.23610] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/20/2014] [Accepted: 03/26/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Alexander Mirzoev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry; Stockholm University; Stockholm SE-10691 Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry; Stockholm University; Stockholm SE-10691 Sweden
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35
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Fu CF, Tian SX. Different aggregation dynamics of benzene–water mixtures. Phys Chem Chem Phys 2014; 16:21957-63. [DOI: 10.1039/c4cp01537a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The differences between the molecular aggregations in benzene–water mixtures are identified using all-atom molecular dynamics simulations.
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Affiliation(s)
- Cen-Feng Fu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics
- University of Science and Technology of China
- Hefei, China
| | - Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics
- University of Science and Technology of China
- Hefei, China
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36
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Dalgicdir C, Sensoy O, Peter C, Sayar M. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition. J Chem Phys 2013; 139:234115. [DOI: 10.1063/1.4848675] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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37
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Ganguly P, van der Vegt NFA. Representability and Transferability of Kirkwood-Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems. J Chem Theory Comput 2013; 9:5247-56. [PMID: 26592264 DOI: 10.1021/ct400242r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We discuss the application of the Kirkwood-Buff iterative Boltzmann inversion (KB-IBI) method for molecular coarse-graining (Ganguly et al. J. Chem. Theory Comput. 2012, 8, 1802) to multicomponent aqueous mixtures. Using a fixed set of effective single-site solvent-solvent potentials previously derived for binary urea-water systems, solute-solvent and solute-solute KB-IBI coarse-grained (CG) potentials have been derived for benzene in urea-water mixtures. Preferential solvation and salting-in coefficients of benzene are reproduced in quantitative agreement with the atomistic force field model. The transferability of the CG models is discussed, and it is shown that free energies of formation of hydrophobic benzene clusters obtained from simulations with the CG model are in good agreement with results obtained from all-atom simulations. The state-point representability of the CG models is discussed with respect to reproducing thermodynamic quantities such as pressure, isothermal compressibility, and preferential solvation. Combined use of KB-IBI and pressure corrections in deriving single-site CG models for pure-water, binary mixtures of urea and water, and ternary mixtures of benzene in urea-water at infinite benzene dilution provides an improved scheme to representing the atomistic pressure and the preferential solvation between the solution components. It is also found that the application of KB-IBI leads to a faster and improved convergence of the pressure and potential energy compared to the IBI method.
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Affiliation(s)
- Pritam Ganguly
- Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
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38
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Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J Phys Chem B 2013; 117:3516-30. [PMID: 23406326 DOI: 10.1021/jp311533p] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hybrid molecular dynamics simulations of atomistic (AA) solutes embedded in coarse-grained (CG) environment can substantially reduce the computational cost with respect to fully atomistic simulations. However, interfacing both levels of resolution is a major challenge that includes a balanced description of the relevant interactions. This is especially the case for polar solvents such as water, which screen the electrostatic interactions and thus require explicit electrostatic coupling between AA and CG subsystems. Here, we present and critically test computationally efficient hybrid AA/CG models. We combined the Gromos atomistic force field with the MARTINI coarse-grained force field. To enact electrostatic coupling, two recently developed CG water models with explicit electrostatic interactions were used: the polarizable MARTINI water model and the BMW model. The hybrid model was found to be sensitive to the strength of the AA-CG electrostatic coupling, which was adjusted through the relative dielectric permittivity εr(AA-CG). Potentials of mean force (PMFs) between pairs of amino acid side chain analogues in water and partitioning free enthalpies of uncharged amino acid side chain analogues between apolar solvent and water show significant differences between the hybrid simulations and the fully AA or CG simulations, in particular for charged and polar molecules. For apolar molecules, the results obtained with the hybrid AA/CG models are in better agreement with the fully atomistic results. The structures of atomistic ubiquitin solvated in CG water and of a single atomistic transmembrane α-helix and the transmembrane portion of an atomistic mechanosensitive channel in CG lipid bilayers were largely maintained during 50-100 ns of AA/CG simulations, partly due to an overstabilization of intramolecular interactions. This work highlights some key challenges on the way toward hybrid AA/CG models that are both computationally efficient and sufficiently accurate for biomolecular simulations.
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Affiliation(s)
- Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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39
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Mirzoev A, Lyubartsev AP. MagiC: Software Package for Multiscale Modeling. J Chem Theory Comput 2013; 9:1512-20. [PMID: 26587613 DOI: 10.1021/ct301019v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present software package MagiC, which is designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modeling of the system in a high resolution (atomistic) description. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated nonbonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the latter accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, allowing parallel simulation of many copies of the system with subsequent averaging of the properties, which provides fast convergence of the method with nearly linear scaling at parallel execution.
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Affiliation(s)
- Alexander Mirzoev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-10691, Sweden
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Schlesier T, Diezemann G. Performance of Different Force Fields in Force Probe Simulations. J Phys Chem B 2013; 117:1862-71. [DOI: 10.1021/jp3115644] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Schlesier
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
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41
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Abstract
This chapter provides a primer on theories for coarse-grained (CG) modeling and, in particular, reviews several systematic methods for determining effective potentials for CG models. The chapter first reviews a statistical mechanics framework for relating atomistic and CG models. This framework naturally leads to a quantitative criterion for CG models that are "consistent" with a particular atomistic model for the same system. This consistency criterion is equivalent to minimizing the relative entropy between the two models. This criterion implies that a many-body PMF is the appropriate potential for a CG model that is consistent with a particular atomistic model. This chapter then presents a unified exposition of the theory and numerical methods for several approaches for approximating this many-body PMF. Finally, this chapter closes with a brief discussion of a few of the outstanding challenges facing the field of systematic coarse-graining.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
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42
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Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications. FROM SINGLE MOLECULES TO NANOSCOPICALLY STRUCTURED MATERIALS 2013. [DOI: 10.1007/12_2013_258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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43
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Zhou SQ, Cheng XC, Jin YL, Wu J, Zhao DS. Molecular dynamics simulation on interacting and mechanical properties of polylactic acid and attapulgite(100) surface. J Appl Polym Sci 2012. [DOI: 10.1002/app.38492] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Mukherjee B, Delle Site L, Kremer K, Peter C. Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. J Phys Chem B 2012; 116:8474-84. [DOI: 10.1021/jp212300d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Biswaroop Mukherjee
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128
Mainz, Germany
| | - Luigi Delle Site
- Institute for Mathematics, Freie Universität Berlin, Arnimallee
6, D-14195 Berlin, Germany
| | - Kurt Kremer
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128
Mainz, Germany
| | - Christine Peter
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128
Mainz, Germany
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45
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Ganguly P, Mukherji D, Junghans C, van der Vegt NFA. Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions. J Chem Theory Comput 2012; 8:1802-7. [DOI: 10.1021/ct3000958] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Pritam Ganguly
- Center of Smart Interfaces,
Technische Universität Darmstadt, Petersenstrasse 32, 64287
Darmstadt, Germany
| | - Debashish Mukherji
- Max-Planck
Institut für
Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Christoph Junghans
- Max-Planck
Institut für
Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
- Theory Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nico F. A. van der Vegt
- Center of Smart Interfaces,
Technische Universität Darmstadt, Petersenstrasse 32, 64287
Darmstadt, Germany
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46
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48
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Engin O, Villa A, Peter C, Sayar M. A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models. MACROMOL THEOR SIMUL 2011. [DOI: 10.1002/mats.201100005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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49
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Shen JW, Li C, van der Vegt NF, Peter C. Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions. J Chem Theory Comput 2011; 7:1916-27. [DOI: 10.1021/ct2001396] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jia-Wei Shen
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Chunli Li
- Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 32, D-64287 Darmstadt, Germany
| | - Nico F.A. van der Vegt
- Center of Smart Interfaces, Technische Universität Darmstadt, Petersenstrasse 32, D-64287 Darmstadt, Germany
| | - Christine Peter
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
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50
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Rzepiela AJ, Louhivuori M, Peter C, Marrink SJ. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys Chem Chem Phys 2011; 13:10437-48. [PMID: 21494747 DOI: 10.1039/c0cp02981e] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein, together with the solvent, is coarse-grained.
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Affiliation(s)
- Andrzej J Rzepiela
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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