Journal ArticleDOI
A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters
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In this article, a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules is presented, which is based on Hill's formal theory of physical clustering.Abstract:
We present a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules. The method is based on Hill’s formal theory of physical clusters. In the method, a molecular dynamics calculation is used to calculate the average potential energy of a cluster of molecules as a function of temperature, and the equilibrium constants are calculated from the integral of the energy with respect to reciprocal temperature. The method is illustrated by calculations of the equilibrium constants for the formation of clusters of two to five water molecules that interact with each other by an intermolecular potential devised by Watts. The method is compared with other procedures for calculating the thermodynamic properties of clusters.read more
Citations
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Canonical sampling through velocity rescaling
TL;DR: In this paper, the authors present a new molecular dynamics algorithm for sampling the canonical distribution, where the velocities of all the particles are rescaled by a properly chosen random factor.
Journal ArticleDOI
SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
TL;DR: In this article, an analytical algorithm called SETTLE for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented, which is based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE.
Journal ArticleDOI
Gromacs 4.5
Sander Pronk,Szilárd Páll,Szilárd Páll,Roland Schulz,Roland Schulz,Per Larsson,Pär Bjelkmar,Pär Bjelkmar,Rossen Apostolov,Rossen Apostolov,Michael R. Shirts,Jeremy C. Smith,Jeremy C. Smith,Peter M. Kasson,David van der Spoel,David van der Spoel,Berk Hess,Berk Hess,Erik Lindahl,Erik Lindahl,Erik Lindahl +20 more
TL;DR: A range of new simulation algorithms and features developed during the past 4 years are presented, leading up to the GROMACS 4.5 software package, which provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
Journal ArticleDOI
Constant pressure molecular dynamics algorithms
TL;DR: In this paper, a modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space averages, and the resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
Journal ArticleDOI
Nosé-Hoover chains : the canonical ensemble via continuous dynamics
TL;DR: In this paper, a modification of the Nose-Hoover dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nose chains, which gives the canonical distribution where the simple formalism fails.
References
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TL;DR: Molecular theory of gases and liquids as mentioned in this paper, molecular theory of gas and liquids, Molecular theory of liquid and gas, molecular theories of gases, and liquid theory of liquids, مرکز
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Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
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TL;DR: In this paper, the authors focus on topics at the forefront of electrochemical research, such as splitting water by electrolysis, splitting water with visible light, and the recent development of lithium batteries.
Journal ArticleDOI
Molecular dynamics simulations at constant pressure and/or temperature
TL;DR: In this paper, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic-isobaric, canonical, and isothermal-isboric ensembles.