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
Bilayer Conformation of Fusion Peptide of Influenza Virus Hemagglutinin: A Molecular Dynamics Simulation Study
TL;DR: Molecular dynamics simulations were performed to investigate the conformation of the 20 amino acids long fusion peptide of influenza hemagglutinin of strain X31 bound to a dimyristoyl phosphatidylcholine bilayer and revealed that the peptide adopts a kinked conformation, in agreement with the NMR structures of a related peptide in detergent micelles.
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Precision of free energies calculated by molecular dynamics simulations of peptides in solution
TL;DR: In this paper, the effects of several factors that may alter the precision are evaluated, such as the length of the simulation, the dependence of the potential energy on λ, the use of conformational restraints, and their magnitude and form.
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Molecular dynamics computer simulations of the effects of hydrogen bonding on the properties of layered double hydroxides intercalated with organic acids
TL;DR: In this article, molecular dynamics simulations of glutamate(1−) and glutamate(2−) intercalated in Mg−Al double hydroxides (LDHs) were performed to understand molecular-level structural, thermodynamic and kinetic aspects of their interactions with LDHs.
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Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
TL;DR: Findings suggest that pancreatic‐like ribonucleases share an evolutionary conserved dynamic behavior consisting of subtle β‐sheet motions, which are essential for substrate binding and release.
Journal ArticleDOI
Soft sticky dipole-quadrupole-octupole potential energy function for liquid water: an approximate moment expansion.
Toshiko Ichiye,Ming-Liang Tan +1 more
TL;DR: The object here is to demonstrate that the SSDQO potentialEnergy function can accurately mimic the potential energy function of a multipoint model using the moments of that model, and the contribution of each moment to the energetics and other properties can be determined.
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.