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
Examining the Contributions of Lipid Shape and Headgroup Charge on Bilayer Behavior
Allison N. Dickey,Roland Faller +1 more
TL;DR: It is found that the Na(+) ion location has a larger effect on bilayer fluidity properties than lipid headgroup size, where the A(lipid) and acyl chain order parameter values are more similar between the PA and PG bilayers that have Na(+ ions located near the ester groups than between the two PA bilayers.
Journal ArticleDOI
A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations
TL;DR: A coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly and reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine- graining atomistic water models.
Journal ArticleDOI
Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions
TL;DR: The effect of helicity on pore stability is investigated at the CG level and it is found that partial helicity is required to form stable pores.
Journal ArticleDOI
Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.
TL;DR: The results complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups), and approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi).
Journal ArticleDOI
Enveloping distribution sampling: a method to calculate free energy differences from a single simulation.
TL;DR: The authors present a method to calculate free energy differences between two states A and B "on the fly" from a single molecular dynamics simulation of a reference state R using Hamiltonian replica-exchange molecular dynamics of the reference state.
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.