Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
Reads0
Chats0
TLDR
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
Citations
More filters
Journal ArticleDOI
Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes
Dirk Matthes,Bert L. de Groot +1 more
TL;DR: Pronounced differences in the propensity of finding prominent secondary structure motifs in the different applied force fields suggest that problems point in particular to the balance of the relative stabilities of helical and extended conformations.
Journal ArticleDOI
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
TL;DR: An atomic detail description of the mechanism by which a protein facilitates specific structural distortion in DNA is presented, which indicates that flipping is facilitated by destabilization of the DNA double-helical structure and substitution of DNA base-pairing and base-stacking interactions with DNA–protein interactions.
Journal ArticleDOI
Collective Langevin dynamics of conformational motions in proteins.
TL;DR: Collective Langevin dynamics (CLD), which evolves the dynamics of the system within a small subspace of relevant collective degrees of freedom, yielded accurate thermodynamical and dynamical behaviors.
Journal ArticleDOI
Structure and dynamics of water confined in a polyamide reverse-osmosis membrane: A molecular-simulation study
TL;DR: In this article, the structural and dynamical properties of water trapped inside a highly cross-linked polyamide RO membrane were investigated and the heterogeneous structure of the membrane was characterized through local water density and cavity size distributions.
Journal ArticleDOI
3D Structure of Torpedo Californica Acetylcholinesterase Complexed with Huprine X at 2. 1 A Resolution: Kinetic and Molecular Dynamic Correlates.
Hay Dvir,Dawn M. Wong,Michal Harel,Xavier Barril,Modesto Orozco,F. J. Luque,Diego Muñoz-Torrero,Pelayo Camps,T. L. Rosenberry,Israel Silman,Joel L. Sussman +10 more
TL;DR: Huprine X is a novel acetylcholinesterase (AChE) inhibitor, with one of the highest affinities reported for a reversible inhibitor, a synthetic hybrid that contains the 4-aminoquinoline substructure of one anti-Alzheimer drug, tacrine, and a carbobicyclic moiety resembling that of another AChE inhibitor, (-)-huperzine A.
References
More filters
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.