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
Computational chemistry from the perspective of numerical analysis
TL;DR: The results of mathematical analysis are outlined, recent results in numerical analysis are laid on, recent developments of new methods and challenging open issues are focused on.
Journal ArticleDOI
Free energy landscape of A-DNA to B-DNA conversion in aqueous solution.
Nilesh K. Banavali,Benoît Roux +1 more
TL;DR: The absolute minimum in the calculated free energy profile corresponds closely to the crystal structure of the hexamer sequence, indicating that the present method has the potential to identify the most stable state for an arbitrary DNA sequence in water.
Journal ArticleDOI
Intercalation processes of copper complexes in DNA.
Rodrigo Galindo-Murillo,Juan Carlos García-Ramos,Lena Ruiz-Azuara,Thomas E. Cheatham,Fernando Cortés-Guzmán,Fernando Cortés-Guzmán +5 more
TL;DR: A molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs.
Journal ArticleDOI
Dynamical Properties of Phospholipid Bilayers from Computer Simulation
Ulrich Essmann,Max L. Berkowitz +1 more
TL;DR: The main emphasis of the present study is on the investigation of the stability over a long time and the dynamic properties of the water/membrane system.
Journal ArticleDOI
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.
TL;DR: The development of the GSBP-based QM/MM protocol has opened up the exciting possibility of studying chemical events in very complex biomolecular systems in a multiscale framework and highlights the importance of carefully treating electrostatics in QM /MM simulations of biomolecules.
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.