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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The good, the bad and the user in soft matter simulations
TL;DR: Vattulainen and Rog as discussed by the authors discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them and provide the reader with a starting point to explore these issues further.
Journal ArticleDOI
Salt bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT
Christopher J. Law,Jonas Almqvist,Adam Bernstein,Regina Goetz,Yafei Huang,Celine Soudant,Aatto Laaksonen,Sven Hovmöller,Da-Neng Wang +8 more
TL;DR: The data suggest that the formation and breaking of inter- and intradomain salt bridges control the conformational change of the transporter that accompanies substrate translocation across the membrane.
Journal ArticleDOI
Estimation of the persistence length of polymers by MD simulations on small fragments in solution. Application to cellulose
TL;DR: In this paper, a procedure is described to estimate the persistence length and related properties of a persistent polymer by MD simulations of a small fragment, including solvent effects, applied to cellulose in aqueous solution.
Journal ArticleDOI
Comparative Molecular Dynamics Studies of Wild-Type and Oxidized Forms of Full-Length Alzheimer Amyloid β-Peptides Aβ(1−40) and Aβ(1−42)
TL;DR: All-atom 50 ns molecular dynamics simulations are performed on the full-length amyloid beta (Abeta) monomers and their oxidized forms and indicate that the WT-Abeta(1-40) monomer adopts an overall beta-hairpin-like structure, which is promoted by the turn region (24-27).
Journal ArticleDOI
Structure of aqueous glucose solutions as determined by neutron diffraction with isotopic substitution experiments and molecular dynamics calculations.
TL;DR: From the comparison of the MD and NDIS data, it was found that while the modeling generally does a satisfactory job in reproducing the experimental data the force fields may produce sugar rings that are too rigid and thus may require future revisions.
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.