Literature DB >> 14978711

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

Michael Patra1, Mikko Karttunen.   

Abstract

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncertainty reflect the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity. We discuss possible implications on the computation of potential of mean force and effective potentials. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 678-689, 2004

Entities:  

Year:  2004        PMID: 14978711     DOI: 10.1002/jcc.10417

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  23 in total

1.  RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.

Authors:  Serdal Kirmizialtin; Suzette A Pabit; Steve P Meisburger; Lois Pollack; Ron Elber
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

2.  Molecular dynamics simulation of water permeation through the alpha-hemolysin channel.

Authors:  Jirasak Wong-Ekkabut; Mikko Karttunen
Journal:  J Biol Phys       Date:  2015-08-12       Impact factor: 1.365

3.  Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions.

Authors:  Wei Zhao; Tomasz Róg; Andrey A Gurtovenko; Ilpo Vattulainen; Mikko Karttunen
Journal:  Biophys J       Date:  2006-11-17       Impact factor: 4.033

4.  Ion leakage through transient water pores in protein-free lipid membranes driven by transmembrane ionic charge imbalance.

Authors:  Andrey A Gurtovenko; Ilpo Vattulainen
Journal:  Biophys J       Date:  2007-01-05       Impact factor: 4.033

Review 5.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

6.  Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity.

Authors:  Emma Falck; Jari T Hautala; Mikko Karttunen; Paavo K J Kinnunen; Michael Patra; Heikki Saaren-Seppälä; Ilpo Vattulainen; Susanne K Wiedmer; Juha M Holopainen
Journal:  Biophys J       Date:  2006-06-16       Impact factor: 4.033

7.  An Investigation of Ion-Pairing of Alkali Metal Halides in Aqueous Solutions Using the Electrical Conductivity and the Monte Carlo Computer Simulation Methods.

Authors:  Jure Gujt; Marija Bešter-Rogač; Barbara Hribar-Lee
Journal:  J Mol Liq       Date:  2014-02       Impact factor: 6.165

8.  Roles of electrostatics and conformation in protein-crystal interactions.

Authors:  Paul V Azzopardi; Jason O'Young; Gilles Lajoie; Mikko Karttunen; Harvey A Goldberg; Graeme K Hunter
Journal:  PLoS One       Date:  2010-02-19       Impact factor: 3.240

9.  Computer simulation of ion cluster speciation in concentrated aqueous solutions at ambient conditions.

Authors:  Sergio A Hassan
Journal:  J Phys Chem B       Date:  2008-08-05       Impact factor: 2.991

10.  Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations.

Authors:  Andrea Catte; James C Patterson; Denys Bashtovyy; Martin K Jones; Feifei Gu; Ling Li; Aldo Rampioni; Durba Sengupta; Timo Vuorela; Perttu Niemelä; Mikko Karttunen; Siewert Jan Marrink; Ilpo Vattulainen; Jere P Segrest
Journal:  Biophys J       Date:  2007-12-07       Impact factor: 4.033

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