Literature DB >> 27802614

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

Xiongwu Wu1, Frank C Pickard1, 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; it folds long-ranged interactions into a short-ranged potential and can be calculated as efficiently as a cutoff method. It has been demonstrated that the IPS method produces consistent simulation results, including free energies, as the particle mesh Ewald (PME) method. By introducing the multipole homogeneous background approximation, this work derives multipole IPS potentials, abbreviated as IPSMm, with m being the maximum order of multipole interactions. To efficiently calculate the multipole interactions in Cartesian space, we propose a vector relation that calculates a multipole tensor as a dot product of a radial potential vector and a directional vector. Using model systems with charges, dipoles, and/or quadrupoles, with and without polarizability, we demonstrate that multipole interactions of order m can be described accurately with the multipole IPS potential of order 2 or m - 1, whichever is higher. Through simulations with the multipole IPS potentials, we examined energetic, structural, and dynamic properties of the model systems and demonstrated that the multipole IPS potentials produce very similar results as PME with a local region radius (cutoff distance) as small as 6 Å.

Entities:  

Year:  2016        PMID: 27802614      PMCID: PMC5085978          DOI: 10.1063/1.4966019

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


  36 in total

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Authors:  N A Baker; V Helms; J A McCammon
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Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

3.  Efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Yihan Shao; Thomas E Cheatham; Bernard R Brooks
Journal:  J Chem Phys       Date:  2015-08-21       Impact factor: 3.488

4.  Atomic-level accuracy in simulations of large protein crystals.

Authors:  D M York; A Wlodawer; L G Pedersen; T A Darden
Journal:  Proc Natl Acad Sci U S A       Date:  1994-08-30       Impact factor: 11.205

5.  Scoring multipole electrostatics in condensed-phase atomistic simulations.

Authors:  Tristan Bereau; Christian Kramer; Fabien W Monnard; Elisa S Nogueira; Thomas R Ward; Markus Meuwly
Journal:  J Phys Chem B       Date:  2013-04-25       Impact factor: 2.991

6.  Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation.

Authors:  Pedro Ojeda-May; Jingzhi Pu
Journal:  J Chem Phys       Date:  2014-04-28       Impact factor: 3.488

7.  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

8.  Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.

Authors:  Celeste Sagui; Lee G Pedersen; Thomas A Darden
Journal:  J Chem Phys       Date:  2004-01-01       Impact factor: 3.488

9.  Application of multipolar charge models and molecular dynamics simulations to study stark shifts in inhomogeneous electric fields.

Authors:  Michael Devereux; Nuria Plattner; Markus Meuwly
Journal:  J Phys Chem A       Date:  2009-11-26       Impact factor: 2.781

10.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

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  3 in total

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

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2019-06-07       Impact factor: 3.488

2.  Critical test of isotropic periodic sum techniques with group-based cut-off schemes.

Authors:  Takuma Nozawa; Kenji Yasuoka; Kazuaki Z Takahashi
Journal:  Sci Rep       Date:  2018-03-08       Impact factor: 4.379

3.  A fast and accurate computational method for the linear-combination-based isotropic periodic sum.

Authors:  Kazuaki Z Takahashi; Takuma Nozawa; Kenji Yasuoka
Journal:  Sci Rep       Date:  2018-08-08       Impact factor: 4.379

  3 in total

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