Literature DB >> 23293678

Non-Ewald methods: theory and applications to molecular systems.

Ikuo Fukuda1, Haruki Nakamura.   

Abstract

Several non-Ewald methods for calculating electrostatic interactions have recently been developed, such as the Wolf method, the reaction field method, the pre-averaging method, and the zero-dipole summation method, for molecular dynamics simulations of various physical systems, including biomolecular systems. We review the theories of these approaches and their potential applications to molecular simulations, and discuss their relationships.

Entities:  

Year:  2012        PMID: 23293678      PMCID: PMC3428531          DOI: 10.1007/s12551-012-0089-4

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  43 in total

1.  Potential of mean force between identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte.

Authors:  Guillermo Iván Guerrero-García; Pedro González-Mozuelos; Mónica Olvera de la Cruz
Journal:  J Chem Phys       Date:  2011-10-28       Impact factor: 3.488

2.  A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics.

Authors:  Prateek K Jha; Rastko Sknepnek; Guillermo Iván Guerrero-García; Monica Olvera de la Cruz
Journal:  J Chem Theory Comput       Date:  2010-10-12       Impact factor: 6.006

3.  Cutoff size does strongly influence molecular dynamics results on solvated polypeptides.

Authors:  H Schreiber; O Steinhauser
Journal:  Biochemistry       Date:  1992-06-30       Impact factor: 3.162

4.  Molecular dynamics study of screening at ionic surfaces.

Authors:  T G Desai
Journal:  J Chem Phys       Date:  2007-10-21       Impact factor: 3.488

5.  Amorphous silica modeled with truncated and screened Coulomb interactions: a molecular dynamics simulation study.

Authors:  Antoine Carré; Ludovic Berthier; Jürgen Horbach; Simona Ispas; Walter Kob
Journal:  J Chem Phys       Date:  2007-09-21       Impact factor: 3.488

6.  Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics.

Authors:  Andrij Baumketner
Journal:  J Chem Phys       Date:  2009-03-14       Impact factor: 3.488

7.  Effects of long-range electrostatic forces on simulated protein folding kinetics.

Authors:  Alex Robertson; Edgar Luttmann; Vijay S Pande
Journal:  J Comput Chem       Date:  2008-04-15       Impact factor: 3.376

8.  Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules.

Authors:  Guillaume Chevrot; Paolo Calligari; Konrad Hinsen; Gerald R Kneller
Journal:  J Chem Phys       Date:  2011-08-28       Impact factor: 3.488

9.  Vibrational sum-frequency generation spectroscopy at the water/lipid interface: molecular dynamics simulation study.

Authors:  Yuki Nagata; Shaul Mukamel
Journal:  J Am Chem Soc       Date:  2010-05-12       Impact factor: 15.419

10.  Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics.

Authors:  Boris Ni; Andrij Baumketner
Journal:  J Mol Model       Date:  2011-02-11       Impact factor: 1.810

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  13 in total

1.  Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.

Authors:  Pedro Ojeda-May; Jingzhi Pu
Journal:  J Chem Phys       Date:  2015-11-07       Impact factor: 3.488

2.  Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Authors:  Gregory A Ross; Ariën S Rustenburg; Patrick B Grinaway; Josh Fass; John D Chodera
Journal:  J Phys Chem B       Date:  2018-05-31       Impact factor: 2.991

3.  Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments.

Authors:  Zaven Ovanesyan; Bharat Medasani; Marcia O Fenley; Guillermo Iván Guerrero-García; Mónica Olvera de la Cruz; Marcelo Marucho
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

4.  Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.

Authors:  Takamasa Arakawa; Narutoshi Kamiya; Haruki Nakamura; Ikuo Fukuda
Journal:  PLoS One       Date:  2013-10-04       Impact factor: 3.240

5.  Multilevel summation method for electrostatic force evaluation.

Authors:  David J Hardy; Zhe Wu; James C Phillips; John E Stone; Robert D Skeel; Klaus Schulten
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

6.  A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex.

Authors:  Kota Kasahara; Ikuo Fukuda; Haruki Nakamura
Journal:  PLoS One       Date:  2014-11-07       Impact factor: 3.240

7.  myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

Authors:  Kota Kasahara; Benson Ma; Kota Goto; Bhaskar Dasgupta; Junichi Higo; Ikuo Fukuda; Tadaaki Mashimo; Yutaka Akiyama; Haruki Nakamura
Journal:  Biophys Physicobiol       Date:  2016-09-07

8.  Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer.

Authors:  Kota Kasahara; Masaaki Shiina; Ikuo Fukuda; Kazuhiro Ogata; Haruki Nakamura
Journal:  PLoS One       Date:  2017-02-23       Impact factor: 3.240

9.  Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.

Authors:  Kota Kasahara; Masaaki Shiina; Junichi Higo; Kazuhiro Ogata; Haruki Nakamura
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

10.  Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization.

Authors:  Maria M Reif; Chris Oostenbrink
Journal:  Theor Chem Acc       Date:  2015-01-10       Impact factor: 1.702

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