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
Temperature dependence of the hydrophobic hydration and interaction of simple solutes: an examination of five popular water models.
TL;DR: Comparing different water models and experimental data is concluded that a proper description of density effects is an important requirement for a water model to account correctly for the correct description of the hydrophobic effects, and aWater model exhibiting a density maximum at the correct temperature is desirable.
Journal ArticleDOI
The mechanism of proton exclusion in the aquaporin-1 water channel
TL;DR: The results indicate that the main barrier in aquaporin-1 is not, as had previously been speculated, caused by the interruption of the hydrogen-bonded water chain, but rather by an electrostatic field centered around the fingerprint Asn-Pro-Ala (NPA) motif.
Journal ArticleDOI
Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations
TL;DR: The two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics simulations is presented, making it an efficient means for extracting thermodynamic properties from MD simulations.
Journal ArticleDOI
Target flexibility: an emerging consideration in drug discovery and design.
Pietro Cozzini,Glen E. Kellogg,Francesca Spyrakis,Donald J. Abraham,Gabriele Costantino,Andrew Emerson,Francesca Fanelli,Holger Gohlke,Leslie A. Kuhn,Garrett M. Morris,Modesto Orozco,Thelma A. Pertinhez,Menico Rizzi,Christoph A. Sotriffer +13 more
TL;DR: Department of General and Inorganic Chemistry, UniVersity of Parma, Via G.P. Usberti 17/A 43100, Parma; Department of Medicinal Chemistry and Institute for Structural Biology & Drug DiscoVery, Virginia Commonwealth Uni Versity, Richmond, Virginia 23298-0540.
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On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: A comparison with experiment
David Poger,Alan E. Mark +1 more
TL;DR: It is shown that the force field reproduces the structure and the hydration of bilayers formed by each of the four lipids with high accuracy and highlights the need to reproduce a broad range of properties beyond the area per lipid, which is poorly defined experimentally.
References
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Book
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Journal ArticleDOI
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Journal ArticleDOI
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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.