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
Computer Simulation of Urea−Water Mixtures: A Test of Force Field Parameters for Use in Biomolecular Simulation
TL;DR: In this paper, a molecular model for urea to be used in conjunction with the simple point charge (SPC) model for liquid water in protein denaturation studies is validated by comparison of molecular dynamics simulation results to experimental data at 298 K as a function of urea mole fraction.
Journal ArticleDOI
Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of the Double-Bond Position
Hector Martinez-Seara,Tomasz Róg,Tomasz Róg,Marta Pasenkiewicz-Gierula,Ilpo Vattulainen,Ilpo Vattulainen,Ilpo Vattulainen,Mikko Karttunen,Ramon Reigada +8 more
TL;DR: A cholesterol-mediated lipid selection mechanism in eukaryotic cell membranes is suggested, which promotes the formation of highly ordered raft-like membrane domains, whereas domains rich in unsaturated lipids with a double bond in the middle remain highly fluid despite the presence of cholesterol.
Journal ArticleDOI
Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules
Maria Fyta,Roland R. Netz +1 more
TL;DR: Using molecular dynamics simulations in conjunction with the SPC/E water model, this work optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs, based on simultaneous optimizing single-ion and ion-pair properties.
Journal ArticleDOI
Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data
Po-chia Chen,Jochen S. Hub +1 more
TL;DR: The present study suggests that quantitative comparison between MD simulations and experimental WAXS profiles emerges as an accurate tool to validate solution ensembles of biomolecules.
Journal ArticleDOI
Lipid Gymnastics: Evidence of Complete Acyl Chain Reversal in Oxidized Phospholipids from Molecular Simulations
TL;DR: This work provides the first molecular evidence of the "extended lipid conformation" in phospholipid membranes, as the chain reversal of PazePC lipids decorates the membrane interface with reactive, negatively charged functional groups.
References
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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
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David Eisenberg,Walter Kauzmann +1 more
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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.