Temperature and Phase Transferable Bottom-up Coarse-Grained Models

被引:37
|
作者
Jin, Jaehyeok [1 ,2 ]
Yu, Alvin [1 ,2 ]
Voth, Gregory A. [1 ,2 ]
机构
[1] Univ Chicago, James Franck Inst, Chicago Ctr Theoret Chem, Dept Chem, Chicago, IL 60637 USA
[2] Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
基金
美国国家科学基金会;
关键词
D O I
10.1021/acs.jctc.0c00832
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
Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the structural correlations in atomistic simulations, the general use of bottom-up CG methods is limited because of the nontransferable nature of these CG models under different thermodynamic conditions. Because bottom-up CG potentials usually correspond to configuration-dependent free energies of the system, recent studies have focused on adjusting enthalpic or entropic contributions to account for issues with transferability. However, these approaches can require a manual adjustment of the CG interaction a priori and are usually limited to constant volume ensembles. To overcome these limitations, we construct temperature and phase transferable CG models under constant pressure by developing the ultra-coarse-graining (UCG) methodology in the mean-field limit. In the mean-field ansatz, an embedded semi-global order parameter recapitulates global changes to the system by automatically adjusting the effective CG interactions, thus bridging free energy decompositions with UCG theory. The method presented is designed to faithfully capture structural correlations under different thermodynamic conditions, using a single UCG model. Specifically, we test the applicability of the developed theory in three distinct cases: (1) different temperatures at constant pressure in liquids, (2) different temperatures across thermodynamic phases, and (3) liquid/vapor interfaces. We demonstrate that the systematic construction of both temperature and phase transferable bottom-up CG models is possible using this generalized UCG theory. Based on our findings, this approach significantly extends the transferability and applicability of the bottom-up CG theory and method.
引用
收藏
页码:6823 / 6842
页数:20
相关论文
共 50 条
  • [1] Bottom-up coarse-grained models for external fields and interfaces
    DeLyser, Michael
    Noid, W. G.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (22):
  • [2] Bottom-Up Coarse-Grained Models for Intrinsically Disordered Proteins
    Dannenhoffer-Lafage, Thomas P.
    Best, Robert B.
    [J]. BIOPHYSICAL JOURNAL, 2021, 120 (03) : 29A - 29A
  • [3] Bottom-Up Coarse-Grained Modeling of DNA
    Sun, Tiedong
    Minhas, Vishal
    Korolev, Nikolay
    Mirzoev, Alexander
    Lyubartsev, Alexander P.
    Nordenskiold, Lars
    [J]. FRONTIERS IN MOLECULAR BIOSCIENCES, 2021, 8
  • [4] Hierarchical Framework for Predicting Entropies in Bottom-Up Coarse-Grained Models
    Jin, Jaehyeok
    Reichman, David R.
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2024, 128 (13): : 3182 - 3199
  • [5] Transferable Coarse-Grained Models for Ionic Liquids
    Wang, Yanting
    Feng, Shulu
    Voth, Gregory A.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5 (04) : 1091 - 1098
  • [6] Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids
    Dunn, Nicholas J. H.
    Noid, W. G.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2015, 143 (24):
  • [7] Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations
    Deichmann, Gregor
    van der Vegt, Nico F. A.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2018, 149 (24):
  • [8] Development of transferable coarse-grained models of amino acids
    Conway, Olivia
    An, Yaxin
    Bejagam, Karteek K.
    Deshmukh, Sanket A.
    [J]. MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2020, 5 (03): : 675 - 685
  • [9] Transferable Mixing of Atomistic and Coarse-Grained Water Models
    Gonzalez, Humberto C.
    Darre, Leonardo
    Pantano, Sergio
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2013, 117 (46): : 14438 - 14448
  • [10] Procedure for Transferable Coarse-Grained Models of Aqueous Polysaccharides
    Sauter, Joerg
    Grafmueller, Andrea
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 13 (01) : 223 - 236