Literature DB >> 27004883

A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system.

Han Wang1, Haruki Nakamura2, Ikuo Fukuda2.   

Abstract

We performed extensive and strict tests for the reliability of the zero-multipole (summation) method (ZMM), which is a method for estimating the electrostatic interactions among charged particles in a classical physical system, by investigating a set of various physical quantities. This set covers a broad range of water properties, including the thermodynamic properties (pressure, excess chemical potential, constant volume/pressure heat capacity, isothermal compressibility, and thermal expansion coefficient), dielectric properties (dielectric constant and Kirkwood-G factor), dynamical properties (diffusion constant and viscosity), and the structural property (radial distribution function). We selected a bulk water system, the most important solvent, and applied the widely used TIP3P model to this test. In result, the ZMM works well for almost all cases, compared with the smooth particle mesh Ewald (SPME) method that was carefully optimized. In particular, at cut-off radius of 1.2 nm, the recommended choices of ZMM parameters for the TIP3P system are α ≤ 1 nm(-1) for the splitting parameter and l = 2 or l = 3 for the order of the multipole moment. We discussed the origin of the deviations of the ZMM and found that they are intimately related to the deviations of the equilibrated densities between the ZMM and SPME, while the magnitude of the density deviations is very small.

Entities:  

Year:  2016        PMID: 27004883     DOI: 10.1063/1.4943956

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


  8 in total

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Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

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Journal:  Protein Sci       Date:  2018-12-20       Impact factor: 6.725

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Authors:  Tahani M Almeleebia; Shahzaib Ahamad; Irfan Ahmad; Ahmad Alshehri; Ali G Alkhathami; Mohammad Y Alshahrani; Mohammed A Asiri; Amir Saeed; Jamshaid Ahmad Siddiqui; Dharmendra K Yadav; Mohd Saeed
Journal:  Front Pharmacol       Date:  2022-08-09       Impact factor: 5.988

7.  Atomic Resolution Homology Models and Molecular Dynamics Simulations of Plasmodium falciparum Tubulins.

Authors:  Kanipakam Hema; Shahzaib Ahamad; Hemant Kumar Joon; Rajan Pandey; Dinesh Gupta
Journal:  ACS Omega       Date:  2021-06-30

8.  Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.

Authors:  Narutoshi Kamiya; Tadaaki Mashimo; Yu Takano; Takahide Kon; Genji Kurisu; Haruki Nakamura
Journal:  Protein Eng Des Sel       Date:  2016-06-21       Impact factor: 1.650

  8 in total

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