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
Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment.
TL;DR: The simulations showed that this protein fragment exhibits distinctly different adsorption behavior on the different surface chemistries, which suggests that surface chemistry can potentially be used to directly control the orientation of adsorbing proteins in a manner that either presents or hides specific bioactive sites contained within a protein's structure.
Journal ArticleDOI
Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study
TL;DR: In this paper, a molecular dynamics simulation of the flexible simple point charge (SPC) and extended SPC/E water models was performed to determine the temperature dependence of the bulk water vibrational spectrum.
Journal ArticleDOI
Orientation of Water Molecules around Small Polar and Nonpolar Groups in Solution: A Neutron Diffraction and Computer Simulation Study
Alan K. Soper,Alenka Luzar +1 more
TL;DR: In this article, the hydrogen/deuterium substitution technique was used to extract the HH (water-H to water-H) pair correlation function, gHH(r), the MM (methyl-H-to methyl-H), gMM(r) and the MH (mixed water-to-mixed DMSO) correlation function gMH(r).
Journal ArticleDOI
Temperature dependence of hydrogen bonding in supercritical water
TL;DR: In this paper, the effect of temperature on hydrogen bonding in supercritical water was investigated at densities of 257 and 659 kg/m3 and at temperatures in the range 773−1073 K using molecular dynamics simulations with a flexible simple point charge water potential.
Journal ArticleDOI
PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues
Sandeep Singh,Harinder Singh,Abhishek Tuknait,Kumardeep Chaudhary,Balvinder Singh,S. Senthil Kumaran,Gajendra P. S. Raghava +6 more
TL;DR: The PEPstrMOD application offers unique advantages that allow the users to predict the structures of peptides having natural residues, non-naturally modified residues, terminal modifications, iv) post-translational modifications, v) D-amino acids and also allows extended simulation of predicted peptides.
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.