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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A novel atom search optimization for dispersion coefficient estimation in groundwater
TL;DR: The experimental results demonstrate that ASO can outperform other well-known approaches such as Particle Swarm Optimization, Genetic Algorithm and Bacterial Foraging Optimization and thatASO is competitive to its competitors for parameter estimation problems.
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Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.
TL;DR: It is suggested that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations and the performance of Bennett's method is particularly striking.
Journal ArticleDOI
Simulation analysis of the stability mutant R96H of T4 lysozyme.
Bruce Tidor,Martin Karplus +1 more
TL;DR: Free energy simulation methods are used to analyze the effects of the mutation Arg 96----His on the stability of T4 lysozyme and it is shown that a number of contributions that stabilize the wild type or the mutant partially cancel in the overall free energy difference.
Journal Article
Reversal of the Hofmeister Series: Specific Ion Effects on Peptides B
Jana Paterová,Kelvin B. Rembert,Jan Heyda,Yadagiri Kurra,HalilI. Okur,Wenshe R. Liu,Christian Hilty,Paul S. Cremer,Pavel Jungwirth +8 more
TL;DR: The present study provides a molecular rationalization of Hofmeister ordering for the anions and provides a route for tuning these interactions by titration or mutation of basic amino acid residues on the protein surface by means of NMR spectroscopy and molecular dynamics simulations.
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Molecular dynamic simulations analysis of ritronavir and lopinavir as SARS-CoV 3CLpro inhibitors
Veena Nukoolkarn,Vannajan Sanghiran Lee,Maturos Malaisree,Ornjira Aruksakulwong,Supot Hannongbua +4 more
TL;DR: To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out and showed that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CLpro.
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.