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
Hydrogen-Bond Kinetics in the Solvation Shell of a Polypeptide
Huafeng Xu,Bruce J. Berne +1 more
TL;DR: In this article, a series of molecular dynamics simulations reveals that the kinetics of breaking and forming water−water hydrogen bonds is slower in the first solvation shell of a 16-residue polypeptide than in bulk water.
Journal ArticleDOI
On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice
Sandeep K. Reddy,Shelby C. Straight,Pushp Bajaj,C. Huy Pham,Marc Riera,Daniel R. Moberg,Miguel A. Morales,Christopher Knight,Andreas W. Götz,Francesco Paesani +9 more
TL;DR: The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase as mentioned in this paper, which has been systematically assessed across the three phases of water through extensive comparisons with experimental data and high level ab initio calculations.
Journal ArticleDOI
The Origin of Layer Structure Artifacts in Simulations of Liquid Water
TL;DR: In this paper, a comparison of different cutoff treatments, namely truncation, reaction field, particle mesh Ewald (PME), and switch and shift functions, for the simulation of water shows that only PME and switch functions yield realistic dipole-dipole interactions at long distance.
Journal ArticleDOI
Temperature and Pressure Dependence of the AMOEBA Water Model
Pengyu Ren,Jay W. Ponder +1 more
TL;DR: In this article, the temperature and pressure dependence of the previously developed polarizable atomic-multipole-based AMOEBA water potential is explored via molecular dynamics simulations at various temperatures ranging from 248 K to 360 K and pressures up to 5000 atm.
Journal ArticleDOI
Structure, Energetics, and Dynamics of Water Adsorbed on the Muscovite (001) Surface: A Molecular Dynamics Simulation
TL;DR: In this article, molecular dynamics simulations of liquid water adsorbed on the muscovite (001) surface provide a greatly increased, atomistically detailed understanding of surface-related effects on water.
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.