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
Transport of a liquid water and methanol mixture through carbon nanotubes under a chemical potential gradient.
TL;DR: This work reports a dual-control-volume grand canonical molecular dynamics simulation study of the transport of a water and methanol mixture under a fixed concentration gradient through nanotubes of various diameters and surface chemistries.
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Direct simulation of electron transfer using ring polymer molecular dynamics: Comparison with semiclassical instanton theory and exact quantum methods
TL;DR: RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force, and provides inadequate quantization of the real-time electronic-state dynamics in the inverted regime.
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A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerases.
Anna Kaisa A.K. Lappi,Marc F. Lensink,Heli I. Alanen,Kirsi E.H. Salo,Mario M. Lobell,André H. Juffer,Lloyd W. Ruddock +6 more
TL;DR: The identification of a conserved arginine residue, located in the loop between beta5 and alpha4 of the catalytic domains of the human protein disulphide isomerase (PDI) family, which is critical for the catalysttic function of PDI, ERp57, ER p72 and P5, specifically for reoxidation is reported.
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Are current atomistic force fields accurate enough to study proteins in crowded environments
Drazen Petrov,Bojan Zagrovic +1 more
TL;DR: In this paper, the authors used explicit-solvent molecular dynamics simulations and a total of 6.4 µs of simulated time to study wild-type and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration.
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Assessing equilibration and convergence in biomolecular simulations
TL;DR: An analysis of peptide simulations to identify the best methods for assessing equilibration and sampling in these systems where there is significant conformational disorder is reported.
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.