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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Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials
TL;DR: In this article, the authors proposed a shell water model with three atoms and an extra particle representing the electronic degrees of freedom, coupled to a dummy position on the bisector of the molecule by a harmonic spring.
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An Ewald summation method for planar surfaces and interfaces
Joseph Hautman,Michael L. Klein +1 more
TL;DR: In this paper, a method for the summation of long range coulomb interactions in systems with periodicity in two dimensions and a finite thickness in the third dimension is presented for simulations of surfaces and interfaces containing charged particles.
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Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations
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Jiaxin Zheng,Guoyu Tan,Peng Shan,Tongchao Liu,Jiangtao Hu,Yancong Feng,Luyi Yang,Ming-Jian Zhang,Zonghai Chen,Yuan Lin,Jun Lu,Joerg C. Neuefeind,Yang Ren,Khalil Amine,Lin-Wang Wang,Kang Xu,Feng Pan +16 more
TL;DR: In this paper, the authors examined the widened window (2.55 V) of a superconcentrated (unsaturated) aqueous solution of LiNO3 through both theoretical and spectral analyses and discovered that a local structure of intimate Li+water interaction arises at super-concentration, generating (Li+(H2O)2)n polymer-like chains to replace the ubiquitous hydrogen bonding between water molecules.
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Comparative Molecular Dynamics Study of Lipid Membranes Containing Cholesterol and Ergosterol
Jacek Czub,Maciej Baginski +1 more
TL;DR: Comparative molecular dynamics simulation of lipid membranes containing human and fungal sterols shows that, compared to cholesterol, ergosterol has higher ordering effect on the phospholipid acyl chains, and can be also utilized in other chemotherapeutic studies on interaction of selected ligands with membranes.
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.