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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Origin of the Difference in Structural Behavior of Poly(acrylic acid) and Poly(methacrylic acid) in Aqueous Solution Discerned by Explicit-Solvent Explicit-Ion MD Simulations
TL;DR: In this article, the conformational and hydration behavior of poly(acrylic acid) and poly(methacrylic acids) in dilute aqueous solution, as a function of charge density, is studied using two different sets of force field parameters: FF-1 and FF-2.
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Asymmetric switching in a homodimeric ABC transporter: a simulation study.
TL;DR: It is shown by molecular dynamics simulation that the initially symmetric structure of Sav1866 readily undergoes asymmetric transitions at its NBSs in a pre-hydrolytic nucleotide configuration, which strengthens recent suggestions that the interplay of a consensus and a degenerate NBS in eukaroytic ABC proteins pre-determines the sequence of hydrolysis at the twoNBSs.
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Markéta Paloncýová,Gabin Fabre,Russell DeVane,Patrick Trouillas,Patrick Trouillas,Karel Berka,Michal Otyepka +6 more
TL;DR: Recommendations are provided for a global, systematic and high throughput thermodynamic evaluations of drugs COSMOmic is a tool of choice due to low computational costs, and Slipids is the force field of choice for studies of more complex systems.
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Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol : Influence of the Treatment of Long-Range Electrostatic Interactions
TL;DR: Eight 100-ns molecular dynamics simulations of a beta-heptapeptide in methanol at 340 K provide clear evidence (continuum electrostatics analysis) for the absence of LS artifacts and some indications for the presence of RF artifacts.
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Fast evaluation of polarizable forces.
Wei Wang,Robert D. Skeel +1 more
TL;DR: Methods that reduce the cost of computing the electrostatic energy and force of a polarizable model from about 7.5 times thecost of computing those of a nonpolarizable model to less than twice the cost are introduced.
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.