Literature DB >> 26589020

Solvent Free Ionic Solution Models from Multiscale Coarse-Graining.

Zhen Cao1, James F Dama1, Lanyuan Lu1, Gregory A Voth1.   

Abstract

Solvent free models for aqueous ionic solutions are derived using the multiscale coarse-graining (MS-CG) method to obtain many-body potentials of mean force and generalized Langevin equations to propagate the model in time. The resulting models are compared to other implicit solvent models for aqueous NaCl in terms of both sampling efficiency and accuracy. First, the equilibrium structural properties of the models are compared, and then the temperature dependence of the interion potentials of mean force are determined to obtain the pairwise entropy associated with the effective ionic interactions. After validating the equilibrium behavior of the new models, the dynamical properties are investigated using generalized Langevin equation dynamics simulations. The dynamical properties can be put into better agreement with the original atomistic models by introducing an exponential memory kernel to account for the strong coupling between the ions and their water solvation shells.

Entities:  

Year:  2012        PMID: 26589020     DOI: 10.1021/ct3007277

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  5 in total

1.  Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.

Authors:  Hung T Nguyen; Naoto Hori; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-30       Impact factor: 11.205

2.  Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.

Authors:  Jaehyeok Jin; Alexander J Pak; Gregory A Voth
Journal:  J Phys Chem Lett       Date:  2019-07-30       Impact factor: 6.475

3.  Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

Authors:  Sandro Bottaro; Kresten Lindorff-Larsen; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-12-10       Impact factor: 6.006

Review 4.  Design and application of implicit solvent models in biomolecular simulations.

Authors:  Jens Kleinjung; Franca Fraternali
Journal:  Curr Opin Struct Biol       Date:  2014-05-20       Impact factor: 6.809

5.  The power of coarse graining in biomolecular simulations.

Authors:  Helgi I Ingólfsson; Cesar A Lopez; Jaakko J Uusitalo; Djurre H de Jong; Srinivasa M Gopal; Xavier Periole; Siewert J Marrink
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-05
  5 in total

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