Coarse-grained molecular models of water: a review

被引:123
|
作者
Hadley, Kevin R. [1 ]
McCabe, Clare [2 ,3 ]
机构
[1] Natl Inst Aerosp, Hampton, VA 23666 USA
[2] Vanderbilt Univ, Dept Chem & Biomol Engn, Nashville, TN 37235 USA
[3] Vanderbilt Univ, Dept Chem, Nashville, TN USA
基金
美国国家科学基金会;
关键词
molecular simulation; anomalies; mapping; force field development; coarse graining; FORCE-FIELD; DYNAMICS SIMULATION; ASSOCIATING FLUIDS; AQUEOUS SOLVATION; PRIMITIVE MODELS; LIPID-BILAYERS; SOLVENT MODEL; POTENTIALS; MESOSCALE; PROTEINS;
D O I
10.1080/08927022.2012.671942
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems involving large time-and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger time steps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regard to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. How the models are parameterised, which typically depends on their application, is also discussed.
引用
收藏
页码:671 / 681
页数:11
相关论文
共 50 条
  • [31] Information-based approach to coarse-grained models in molecular biophysics
    Shell, M. Scott
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012, 244
  • [32] RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models
    Leonarski, Filip
    Trylska, Joanna
    BIOPHYSICAL JOURNAL, 2015, 108 (08) : 1843 - 1847
  • [33] Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane
    Szklarczyk, Oliwia M.
    Arvaniti, Eirini
    van Gunsteren, Wilfred F.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2015, 36 (17) : 1311 - 1321
  • [34] Coarse-Grained Models Reveal Functional Dynamics - II. Molecular Dynamics Simulation at the Coarse-Grained Level - Theories and Biological Applications
    Chng, Choon-Peng
    Yang, Lee-Wei
    BIOINFORMATICS AND BIOLOGY INSIGHTS, 2008, 2 : 171 - 185
  • [35] Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
    Zavadlav, Julija
    Melo, Manuel N.
    Marrink, Siewert J.
    Praprotnik, Matej
    JOURNAL OF CHEMICAL PHYSICS, 2015, 142 (24):
  • [36] Ionomer Dispersions in Water/Alcohol Solutions by Coarse-Grained Molecular Dynamics
    Mabuchi, T.
    Tokumasu, T.
    POLYMER ELECTROLYTE FUEL CELLS 17 (PEFC 17), 2017, 80 (08): : 577 - 581
  • [37] Molecular Simulation of Lipids and Water: Atomistic, Coarse-Grained, and Mixed Resolutions
    Orsi, Mario
    Ding, Wei
    Palaiokostas, Michail
    Wang, Wen
    BIOPHYSICAL JOURNAL, 2016, 110 (03) : 413A - 413A
  • [38] Representability and Dynamical Consistency in Coarse-Grained Models
    Banos, Manuel Palma
    Popov, Alexander V.
    Hernandez, Rigoberto
    JOURNAL OF PHYSICAL CHEMISTRY B, 2024, 128 (06): : 1506 - 1514
  • [39] Developing coarse-grained models for agglomerate growth
    Milena Smiljanic
    Rudolf Weeber
    Dirk Pflüger
    Christian Holm
    Andreas Kronenburg
    The European Physical Journal Special Topics, 2019, 227 : 1515 - 1527
  • [40] Sequence design in coarse-grained protein models
    Irbäck, A
    PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT, 2000, (138): : 273 - 281