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
Citations
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Journal ArticleDOI
Computing the Kirkwood g-Factor by Combining Constant Maxwell Electric Field and Electric Displacement Simulations: Application to the Dielectric Constant of Liquid Water.
TL;DR: This work shows a simple approach to extract the short-ranged Kirkwood g-factor from molecular dynamics (MD) simulation by superposing the outcomes of constant electric field E and constant electric displacement D simulations and computed the bulk dielectric constant of liquid water modeled in the generalized gradient approximation (PBE) to density functional theory.
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On the approximation of solvent effects on the conformation and dynamics of cyclosporin a by stochastic dynamics simulation techniques
TL;DR: In this article, the molecular simulation technique of stochastic dynamics (SD) is tested by application to the immunosuppressive drug cyclosporin A (CPA).
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Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model.
Thomas Stockner,Therese Montgomery,Oliver Kudlacek,René Weissensteiner,Gerhard F. Ecker,Michael Freissmuth,Harald H. Sitte +6 more
TL;DR: The high-affinity zinc binding site endogenously present in DAT was exploited to create a model of the complete transmemberane domain of DAT, providing a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.
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Effects of Ca2+ on supramolecular aggregation of natural organic matter in aqueous solutions: A comparison of molecular modeling approaches
Andrey G. Kalinichev,Eugenia Iskrenova-Tchoukova,Won Young Ahn,Mark M. Clark,R. James Kirkpatrick +4 more
TL;DR: In this paper, the authors report and analyze three molecular dynamics simulations of Ca2+ complexation with NOM in aqueous solutions in an attempt to quantitatively assess possible effects of model-and system size-dependence in such simulations.
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Proton momentum distribution in water: an open path integral molecular dynamics study.
TL;DR: An extension of the staging path integral molecular dynamics method is presented, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases, utilizing a flexible, single point charge empirical force field to model the system's interactions.
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.