Literature DB >> 31176325

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation.

Xiongwu Wu1, Bernard R Brooks1.   

Abstract

Isotropic periodic sum (IPS) is a method to calculate long-range interactions based on the homogeneity of simulation systems. By using the isotropic periodic images of a local region to represent remote structures, long-range interactions become a function of the local conformation. This function is called the IPS potential, which folds long-ranged interactions into a short-ranged potential and can be calculated as efficiently as a cutoff method. Analytic solutions of IPS potentials have been solved for many interaction types. To further simplify the application of the IPS method, this work presents the homogeneity condition, which requires the sum of interaction energies for any particle to be independent of cutoff distances for a truly homogeneous system. Using the homogeneity condition, one can avoid the complicated mathematic work to solve analytic solutions and can instead use simple functions as IPS potentials. Example simulations are performed for model systems of a series of interaction types. Energies, volumes, and their fluctuations from these simulations demonstrate that simple IPS potentials obtained through the homogeneity condition can satisfactorily describe long-range interactions. The homogeneity condition makes the IPS method a convenient way to handle long-range interactions of any type.

Entities:  

Year:  2019        PMID: 31176325      PMCID: PMC6551215          DOI: 10.1063/1.5097560

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


  18 in total

Review 1.  Connecting local structure to interface formation: a molecular scale van der Waals theory of nonuniform liquids.

Authors:  John D Weeks
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

2.  Cutoff radius effect of the isotropic periodic sum method in homogeneous system. II. Water.

Authors:  Kazuaki Takahashi; Tetsu Narumi; Kenji Yasuoka
Journal:  J Chem Phys       Date:  2010-07-07       Impact factor: 3.488

3.  Gaussian split Ewald: A fast Ewald mesh method for molecular simulation.

Authors:  Yibing Shan; John L Klepeis; Michael P Eastwood; Ron O Dror; David E Shaw
Journal:  J Chem Phys       Date:  2005-02-01       Impact factor: 3.488

4.  Isotropic periodic sum: a method for the calculation of long-range interactions.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2005-01-22       Impact factor: 3.488

5.  Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid.

Authors:  Kazuaki Takahashi; Kenji Yasuoka; Tetsu Narumi
Journal:  J Chem Phys       Date:  2007-09-21       Impact factor: 3.488

6.  Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2008-10-21       Impact factor: 3.488

7.  Fast multipole methods for particle dynamics.

Authors:  J Kurzak; B M Pettitt
Journal:  Mol Simul       Date:  2006       Impact factor: 2.178

8.  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

9.  Correct virial formulation in the isotropic periodic sum method.

Authors:  Iordan H Hristov; Reginald Paul; Stephen J Paddison
Journal:  J Chem Phys       Date:  2009-10-28       Impact factor: 3.488

10.  Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.

Authors:  Richard M Venable; Linda E Chen; Richard W Pastor
Journal:  J Phys Chem B       Date:  2009-04-30       Impact factor: 2.991

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