Literature DB >> 23145717

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions.

Rolf E Isele-Holder1, Wayne Mitchell, Ahmed E Ismail.   

Abstract

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation of these contributions, we have implemented a particle-particle particle-mesh Ewald solver for dispersion (r(-6)) interactions into the LAMMPS molecular dynamics package. We demonstrate that the solver's O(N log N) scaling behavior allows its application to large-scale simulations. We carefully determine a set of parameters for the solver that provides accurate results and efficient computation. We perform a series of simulations with Lennard-Jones particles, SPC/E water, and hexane to show that with our choice of parameters the dependence of physical results on the chosen cutoff radius is removed. Physical results and computation time of these simulations are compared to results obtained using either a plain cutoff or a traditional Ewald sum for dispersion.

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Year:  2012        PMID: 23145717     DOI: 10.1063/1.4764089

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


  11 in total

1.  Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors.

Authors:  Dejun Lin
Journal:  J Chem Phys       Date:  2015-09-21       Impact factor: 3.488

2.  Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation.

Authors:  Qianjun Liu; Guodong Hu; Zanxia Cao; Jihua Wang; Haifeng Chen
Journal:  J Mol Model       Date:  2015-04-26       Impact factor: 1.810

3.  Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Authors:  Alison N Leonard; Andrew C Simmonett; Frank C Pickard; Jing Huang; Richard M Venable; Jeffery B Klauda; Bernard R Brooks; Richard W Pastor
Journal:  J Chem Theory Comput       Date:  2018-01-09       Impact factor: 6.006

4.  Best Practices for Foundations in Molecular Simulations [Article v1.0].

Authors:  Efrem Braun; Justin Gilmer; Heather B Mayes; David L Mobley; Jacob I Monroe; Samarjeet Prasad; Daniel M Zuckerman
Journal:  Living J Comput Mol Sci       Date:  2018-11-29

5.  Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Authors:  Yalun Yu; Andreas Krämer; Richard M Venable; Andrew C Simmonett; Alexander D MacKerell; Jeffery B Klauda; Richard W Pastor; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

6.  Effect of external electric field on nanobubbles at the surface of hydrophobic particles during air flotation.

Authors:  Leichao Wu; Yong Han; Qianrui Zhang; Shuai Zhao
Journal:  RSC Adv       Date:  2019-01-14       Impact factor: 4.036

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Authors:  Ming Chu; Ran Ding; Zheng-yun Chu; Ming-bo Zhang; Xiao-yan Liu; Shao-hua Xie; Yan-jun Zhai; Yue-dan Wang
Journal:  BMC Complement Altern Med       Date:  2014-03-06       Impact factor: 3.659

8.  Sparsification of long range force networks for molecular dynamics simulations.

Authors:  Peter Woerner; Aditya G Nair; Kunihiko Taira; William S Oates
Journal:  PLoS One       Date:  2019-04-12       Impact factor: 3.240

9.  A molecular picture of surface interactions of organic compounds on prevalent indoor surfaces: limonene adsorption on SiO2.

Authors:  Yuan Fang; Pascale S J Lakey; Saleh Riahi; Andrew T McDonald; Mona Shrestha; Douglas J Tobias; Manabu Shiraiwa; Vicki H Grassian
Journal:  Chem Sci       Date:  2019-01-09       Impact factor: 9.825

10.  Exploration of the cofactor specificity of wild-type phosphite dehydrogenase and its mutant using molecular dynamics simulations.

Authors:  Kunlu Liu; Min Wang; Yubo Zhou; Hongxiang Wang; Yudong Liu; Lu Han; Weiwei Han
Journal:  RSC Adv       Date:  2021-04-19       Impact factor: 3.361

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