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
Algorithmic Challenges in Computational Molecular Biophysics
Tamar Schlick,Robert D. Skeel,Axel T. Brunger,Laxmikant V. Kale,John A. Board,Jan Hermans,Klaus Schulten +6 more
TL;DR: A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions.
Journal ArticleDOI
Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop.
TL;DR: The calculated free energy difference of 80 kJ/mol between the minimum of the PMF and the value in water agrees well with thefree energy difference calculated from the experimentally measured critical micelle concentration, suggesting lipid flip-flop and basal permeability of ions are pore mediated.
Journal ArticleDOI
Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations
TL;DR: Force-probe molecular dynamics simulations were used to obtain insight into the tension-induced activation mechanism of titin kinase and find evidence for a sequential mechanically induced opening of the catalytic site without complete domain unfolding.
Journal ArticleDOI
Static and Dynamical Properties of Liquid Water from First Principles by a Novel Car−Parrinello-like Approach
TL;DR: This work assesses the accuracy of ab initio molecular dynamics at the semilocal density functional level of theory to describe structural and dynamic properties of liquid water at ambient conditions and can estimate both the thermodynamic value of the diffusion coefficient and the shear viscosity.
Journal ArticleDOI
Molecular Dynamics Simulation of Amyloid β Dimer Formation
Brigita Urbanc,Luis Cruz,Feng Ding,Feng Ding,Deanne W. Sammond,Sagar D. Khare,Sergey V. Buldyrev,H. E. Stanley,Nikolay V. Dokholyan +8 more
TL;DR: In this paper, a molecular dynamics approach was introduced to study amyloid b (Ab) dimer formation, using discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations; and employing all-atom molecular mechanics simulations to estimate thermodynamic stability of all the conformations.
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.