Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
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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.About:
This article is published in Journal of Computational Physics.The article was published on 1977-03-01 and is currently open access. It has received 18394 citations till now. The article focuses on the topics: Generalized coordinates & Holonomic constraints.read more
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Effects of Water Concentration on the Structural and Diffusion Properties of Imidazolium-Based Ionic Liquid–Water Mixtures
TL;DR: The authors' simulations revealed major structural changes consistent with a transition from IL-water mixture to aqueous solution in all three ILs at water concentrations around 75 mol %, including rapid increase in the frequency of hydrogen bonds and sudden decrease in cationic stacking at the transition point.
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How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations
TL;DR: Experimental and theoretical analyses of the role of changes in HIV reverse transcriptase structure in selecting a correct substrate are presented and atomically detailed simulations using the Milestoning method predict a rate and free energy profile of the conformational change commensurate with experimental data.
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Constant pressure-constant temperature molecular dynamics for rigid and partially rigid molecular systems
TL;DR: In this paper, the method of molecular dynamics at fixed pressure and/or temperature is adapted to rigid or partly rigid molecular systems with geometrical constraints using the cartesian coordinate approach.
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Accuracy assessment and automation of free energy calculations for drug design.
Clara D. Christ,Thomas R. Fox +1 more
TL;DR: The average accuracy of free energy calculations for a total of 92 ligands binding to five different targets was assessed and Analytical uncertainty estimates calculated from a single free energy calculation were found to be much smaller than the sample standard deviation obtained from two independentfree energy calculations.
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Substrate specificity of prostate-specific antigen (PSA)
Gary S. Coombs,Robert C. Bergstrom,Jean-Luc Pellequer,Scott I. Baker,Marc Navre,Matthew M. Smith,John A. Tainer,Edwin L. Madison,David R. Corey +8 more
TL;DR: The importance of secondary subsites in defining both the specificity and efficiency of cleavage suggests that substrate recognition by PSA is mediated by an extended binding site, which should facilitate the development of more sensitive activity-based assays and the design of potent inhibitors.
References
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Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.
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Improved simulation of liquid water by molecular dynamics
TL;DR: In this paper, a four-charge model for each molecule and a modification of the prior ''BNS'' interaction was proposed to improve the fidelity of the molecular dynamics simulation, leading to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x-ray scattering experiments.
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Molecular Dynamics Study of Liquid Water
TL;DR: In this paper, a sample of water, consisting of 216 rigid molecules at mass density 1 gm/cm3, has been simulated by computer using the molecular dynamics technique, subject to an effective pair potential that incorporates the principal structural effects of manybody interactions in real water.
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Molecular dynamics of liquid n-butane near its boiling point
TL;DR: The self-diffusion coefficient of n-butane is approximately 6.0 × 10−5 cm2/s and the corresponding velocity autocorrelation function displays practically no cage effect, differing markedly from argon and other simple fluids.
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Simulation of Diatomic Homonuclear Liquids
TL;DR: In this paper, the authors used the molecular-dynamic method to simulate a fluid of 500 rigid diatomic homo-nuclear molecules interacting by a double Lennard-Jones potential.