Literature DB >> 18366209

Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials.

Sergei Izvekov1, Jessica M J Swanson, Gregory A Voth.   

Abstract

A short-range effective potential for long-range electrostatic interactions in homogeneously disordered condensed phase systems has been determined with a novel approach to coarse-graining in interaction space. As opposed to coarse-graining the system resolution, this approach "coarsens" the system's interactions by mapping multiple configurations of an accurate long-range atomistic potential onto a more efficient, short-range effective potential with a force-matching (FM) method. Developing an empirical potential in this manner is fundamentally different from existing strategies because it utilizes condensed-phase (as opposed to gas-phase) atomistic interactions to determine general pair potentials defined on distance meshes (as opposed to fitting predetermined functional forms). The resulting short-range ( approximately 10 A) effective potential reproduces structural, dynamical, and many thermodynamic properties of liquid water, ions in water, and hydrophobes in water, with unprecedented accuracy. The effective potential is also shown to be transferable to a nonaqueous molten salt system. With continued development, such effective potentials may provide an accurate and highly efficient alternative to Ewald-based long-range electrostatics methods.

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Year:  2008        PMID: 18366209     DOI: 10.1021/jp710339n

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  14 in total

1.  Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water.

Authors:  Jocelyn M Rodgers; John D Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-08       Impact factor: 11.205

2.  The ruggedness of protein-protein energy landscape and the cutoff for 1/r(n) potentials.

Authors:  Anatoly M Ruvinsky; Ilya A Vakser
Journal:  Bioinformatics       Date:  2009-02-23       Impact factor: 6.937

3.  Comparative atomistic and coarse-grained study of water: what do we lose by coarse-graining?

Authors:  Han Wang; Christoph Junghans; Kurt Kremer
Journal:  Eur Phys J E Soft Matter       Date:  2009-01-14       Impact factor: 1.890

Review 4.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

5.  Isotropic periodic sum of electrostatic interactions for polar systems.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

6.  Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor.

Authors:  Xiongwu Wu; Frank C Pickard; Bernard R Brooks
Journal:  J Chem Phys       Date:  2016-10-28       Impact factor: 3.488

7.  CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.

Authors:  Kiersten M Ruff; Tyler S Harmon; Rohit V Pappu
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

8.  On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties.

Authors:  Kevin R Hadley; Clare McCabe
Journal:  J Phys Chem B       Date:  2010-04-08       Impact factor: 2.991

9.  Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

Authors:  Takefumi Yamashita; Yuxing Peng; Chris Knight; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

10.  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

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