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
Simulations of transient membrane behavior in cells subjected to a high-intensity ultrashort electric pulse
Q. Hu,S. Viswanadham,Ravindra P. Joshi,Karl H. Schoenbach,Stephen J. Beebe,Peter F. Blackmore +5 more
TL;DR: The present simulations demonstrate that ions could facilitate pore formation and have direct relevance to the recent observations of calcium release from the endoplasmic reticulum in cells subjected to such ultrashort, high-intensity pulses.
Journal ArticleDOI
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer
TL;DR: It is shown that AMBER99 strongly favors helical structures for the monomer and does not predict any β-sheet structure for the dimer and trimer, while OPLS predicts diverse structures and the free energy landscapes obtained by three force fields are very different.
Journal ArticleDOI
Algorithms for constrained molecular dynamics
TL;DR: The form of the nonlinear equations is examined in detail and used to give convergence results for the traditional nonlinear solution technique SHAKE iteration and for a modification based on successive overrelaxation (SOR).
Journal ArticleDOI
Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore
TL;DR: It is proposed that selective permeation from the intracellular side primarily results from a large energy barrier blocking filter entry for Na+ and Li+ in the presence of K+, not from a difference of binding affinity between ions.
Journal ArticleDOI
Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure
Ross A. Lippert,Cristian Predescu,Douglas J. Ierardi,Kenneth M. Mackenzie,Michael P. Eastwood,Ron O. Dror,David E. Shaw +6 more
TL;DR: This work presents a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostats and barostats to be applied infrequently and reduces software complexity and improves software modularity.
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.