Literature DB >> 22651887

Water structure-forming capabilities are temperature shifted for different models.

Roman Shevchuk1, Diego Prada-Gracia, Francesco Rao.   

Abstract

A large number of water models exist for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient. Past analysis mostly concentrated on ensemble quantities, while few data were reported on the different microscopic behavior. Here, we compare seven widely used classical water models (SPC, SPC/E, TIP3P, TIP4P, TIP4P-Ew, TIP4P/2005, and TIP5P) in terms of their local structure-forming capabilities through hydrogen bonds for temperatures ranging from 210 to 350 K by the introduction of a set of order parameters taking into account the configuration of up to the second solvation shell. We found that all models share the same structural pattern up to a temperature shift. When this shift is applied, all models overlap onto a master curve. Interestingly, increased stabilization of fully coordinated structures extending to at least two solvation shells is found for models that are able to reproduce the correct position of the density maximum. Our results provide a self-consistent atomic-level structural comparison protocol, which can be of help in elucidating the influence of different water models on protein structure and dynamics.

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Year:  2012        PMID: 22651887     DOI: 10.1021/jp303583f

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


  2 in total

1.  Engineering complementary hydrophobic interactions to control β-hairpin peptide self-assembly, network branching, and hydrogel properties.

Authors:  Sameer Sathaye; Huixi Zhang; Cem Sonmez; Joel P Schneider; Christopher M MacDermaid; Christopher D Von Bargen; Jeffery G Saven; Darrin J Pochan
Journal:  Biomacromolecules       Date:  2014-10-17       Impact factor: 6.988

2.  Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.

Authors:  Luan Carvalho Martins; Pedro Henrique Monteiro Torres; Renata Barbosa de Oliveira; Pedro Geraldo Pascutti; Elio A Cino; Rafaela Salgado Ferreira
Journal:  J Comput Aided Mol Des       Date:  2018-03-21       Impact factor: 3.686

  2 in total

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