Literature DB >> 19624176

The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation.

Avisek Das1, Hans C Andersen.   

Abstract

The multiscale coarse-graining (MS-CG) method, proposed by Izvekov and Voth [J. Phys. Chem. B 109, 2469 (2005); Izvekov and VothJ. Chem. Phys. 123, 134105 (2005)], is a method for determining the effective potential energy function for a coarse-grained model of a fluid using data obtained from molecular dynamics (MD) simulation of the corresponding atomically detailed model. The method has been given a rigorous statistical mechanical basis [Noid et al. J. Chem. Phys. 128, 244114 (2008); Noid et al., J. Chem. Phys. 128, 244115 (2008)]. The coarse-grained (CG) potentials obtained using the MS-CG method are an approximate variational solution for the exact many-body potential of mean force for the coarse-grained sites. In this paper we apply this method to study the many-body potential of mean force among solutes in a simple model of a solution of Lennard-Jones particles. We use a new set of basis functions for the variational calculation that is useful when the coarse-grained potential is approximately equal to an arbitrarily complicated pairwise additive, central interaction among the sites of the coarse-grained model. For this model, pairwise additivity of the many-body potential of mean force is a very good approximation when the solute concentration is low, and it becomes less accurate for high concentrations, indicating the importance of many-body contributions to the coarse-grained potential. The best possible pairwise additive CG potential of the solute particles is found to be quite long ranged for all concentrations except those for which the mole fraction of solute is very close to unity. We discuss strategies for construction of short-ranged potentials for efficient but accurate CG MD simulation. We also discuss how the choice of basis functions for the variational calculation can be used to provide smoothing of the calculated CG potential function to overcome statistical sampling error in the atomistic simulation data used for the generation of the potential.

Entities:  

Year:  2009        PMID: 19624176     DOI: 10.1063/1.3173812

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

1.  A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent.

Authors:  Jason A Wagoner; Vijay S Pande
Journal:  J Chem Phys       Date:  2011-06-07       Impact factor: 3.488

2.  Multiscale simulation of microbe structure and dynamics.

Authors:  Harshad Joshi; Abhishek Singharoy; Yuriy V Sereda; Srinath C Cheluvaraja; Peter J Ortoleva
Journal:  Prog Biophys Mol Biol       Date:  2011-07-23       Impact factor: 3.667

3.  Communication: Adaptive boundaries in multiscale simulations.

Authors:  Jason A Wagoner; Vijay S Pande
Journal:  J Chem Phys       Date:  2018-04-14       Impact factor: 3.488

Review 4.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

5.  A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.

Authors:  Anand Srivastava; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

6.  Model reduction of rigid-body molecular dynamics via generalized multipole potentials.

Authors:  Paul N Patrone; Andrew Dienstfrey; G B McFadden
Journal:  Phys Rev E       Date:  2019-12       Impact factor: 2.529

7.  Bayesian calibration of coarse-grained forces: Efficiently addressing transferability.

Authors:  Paul N Patrone; Thomas W Rosch; Frederick R Phelan
Journal:  J Chem Phys       Date:  2016-04-21       Impact factor: 3.488

  7 in total

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