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
Position‐resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
TL;DR: Here, position‐dependent free energies of solvation for all amino acid analogs along the membrane normal are presented and produced from all‐atom molecular dynamics simulations to provide the spatial resolution currently not available from experiments.
Journal ArticleDOI
Computational evaluation of the reactivity and pharmaceutical potential of an organic amine: A DFT, molecular dynamics simulations and molecular docking approach.
Christina Susan Abraham,S. Muthu,Johanan Christian Prasana,Stevan Armaković,Sanja J. Armaković,B. Fathima Rizwana,Ben Geoffrey,R. Host Antony David +7 more
TL;DR: The first hyperpolarizability which is an important parameter for future studies of nonlinear optics (NLO) was calculated to check the potential of the molecule to be an NLO material and a comparison of the physiochemical parameters of PIDAA and commercially available drugs was carried out.
Journal ArticleDOI
Wetting of nanogrooved polymer surfaces.
TL;DR: The composite solid-liquid contact, which is preferred in practical applications and in which a droplet rests on top of the surface asperities, was observed on the roughest PE surfaces, whereas water filled the similar but slightly deeper grooves on PVC surfaces.
Journal ArticleDOI
A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol.
TL;DR: The 53A6OXY+D set reproduces well the QM rotational profiles of DXE in vacuum, the conformational populations ofDXE in the pure liquid and in aqueous mixtures, and the experimental thermodynamic pure-liquid and (polar and nonpolar) solvation properties of DME, DEE, MPH, and DXE.
Journal ArticleDOI
Pressure calculation in polar and charged systems using Ewald summation: Results for the extended simple point charge model of water
TL;DR: In this paper, the authors compared the virial and thermodynamic pressure for the extended simple point charge (SPC/E) water model at standard conditions, and found that the thermodynamic pressures exhibit considerably less system size dependence than the Virial pressure.
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.