Book ChapterDOI
Interaction Models for Water in Relation to Protein Hydration
Hjc Berendsen,J. P. M. Postma,W. F. van Gunsteren,Jan Hermans +3 more
- pp 331-342
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TLDR
In this article, a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6-12 potential on the oxygen positions only was developed, and parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion.Abstract:
For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.read more
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Journal ArticleDOI
Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore
Gustavo Troiano Feliciano,Gustavo Troiano Feliciano,C F Sanz-Navarro,Maurício D. Coutinho-Neto,Pablo Ordejón,Ralph H. Scheicher,Alexandre Reily Rocha +6 more
TL;DR: In this paper, the influence of the solvent on the dynamics of DNA and the resulting electron transport properties of a prototypic sequencing device utilizing a graphene nanopore through which the nucleic-acid chain is threaded.
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A short guide for molecular dynamics simulations of RNA systems.
Yaser Hashem,Pascal Auffinger +1 more
TL;DR: Practical guidelines for the setup of MD simulations, the choice of ionic conditions and the detection and correction of experimental inaccuracies in order to start MD simulations of nucleic acid systems under the best auspices are provided.
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Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations
Elena Heikkilä,Elena Heikkilä,Hector Martinez-Seara,Andrey A. Gurtovenko,Andrey A. Gurtovenko,Matti Javanainen,Hannu Häkkinen,Ilpo Vattulainen,Ilpo Vattulainen,Jaakko Akola,Jaakko Akola,Jaakko Akola +11 more
TL;DR: In this article, atomistic simulations of cationic Au nanoparticles interacting with realistic membranes and explicit solvent using a model system that comprises two cellular compartments, extracellular and cytosolic, divided by two asymmetric lipid bilayers.
Journal ArticleDOI
Water–Carbon Interactions 2: Calibration of Potentials using Contact Angle Data for Different Interaction Models
TL;DR: In this paper, the effects of adding C-H Lennard-Jones interactions and changing the long-range cut-off distance are considered for the discrete graphite surface model studied by Werder et al.
Journal ArticleDOI
Adsorption of Leucine-Rich Amelogenin Protein on Hydroxyapatite (001) Surface through -COO - Claws
TL;DR: In this article, simulations of the dynamic behavior of six different orientations of leucine-rich amelogenin protein (LRAP) on a fixed hydrophilic HAP surface (001) were performed.
References
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Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
Book
The Structure and Properties of Water
David Eisenberg,Walter Kauzmann +1 more
TL;DR: The Water Molecule 2 The Real Vapour 3. Ice 4. Properties of Liquid Water 5. Models for Liquid Water Addendum as mentioned in this paper, which is an extension of the model presented in this paper.
Journal ArticleDOI
Dynamics of folded proteins
TL;DR: The dynamics of a folded globular protein have been studied by solving the equations of motion for the atoms with an empirical potential energy function and suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.
Journal ArticleDOI
Algorithms for macromolecular dynamics and constraint dynamics
TL;DR: In this paper, the authors investigated the application of the computer simulation method of molecular dynamics to macromolecules and compared different algorithms for integrating the equations of motion, both theoretically and in practice.