相关论文: Generating Generalized Distributions from Dynamica…

This article proposes a novel thermostat applicable to any particle-based dynamic simulation. Each pair of particles is thermostated either (with probability P) with a pairwise Lowe-Andersen thermostat, or (with probability 1-P) with a…

The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in…

The widely used Nose-Hoover chain (NHC) thermostat in molecular dynamics simulations is generally believed to impart the canonical distribution as well as quasi- (i.e., space filling) ergodicity on the thermostatted physical system (PS).…

In this paper we formulate Bulgac-Kusnezov constant temperature dynamics in phase space by means of non-Hamiltonian brackets. Two generalized versions of the dynamics are similarly defined: one where the Bulgac-Kusnezov demons are globally…

We show a unified second-order scheme for constructing simple, robust and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB…

"Pedagogical derivations for Nos\'e's dynamics can be developed in two different ways, (i) by starting with a temperature-dependent Hamiltonian in which the variable $s$ scales the time or the mass, or (ii) by requiring that the equations…

We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev.…

Thermostated tethered harmonic lattices provide good illustrations of the phase-space dimensionality loss which occurs in the strange-attractor distributions characterizing stationary nonequilibrium flows. We use time-reversible…

We present an ab initio stochastic method for calculating thermal properties of a trapped, 1D Bose-gas covering the whole range from weak to strong interactions. Discretization of the problem results in a Bose-Hubbard-like Hamiltonian,…

We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods…

Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…

With this work we present two new methods for the generation of thermostated, manifestly Hamiltonian dynamics and provide corresponding illustrations. The basis for this new class of thermostats are the peculiar thermodynamics as exhibited…

In this work we present a calculation of the hamiltonian variables solving the molecular dynamics equations of motion for a system of nuclear matter relevant to the description of nuclear pasta. The temperature is kept fixed by using the…

In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…

I review recent results from numerical simulations on the structure and dynamics of the ISM, and attempt to put together a coherent dynamical scenario. In particular, I discuss results on 1) the spatial distribution of the gas components,…

The numerical integration of the Nose-Hoover dynamics gives a deterministic method that is used to sample the canonical Gibbs measure. The Nose-Hoover dynamics extends the physical Hamiltonian dynamics by the addition of a "thermostat"…

The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…

One-variable thermostats are studied as a generalization of the Nos\'e--Hoover method which is aimed to achieve Gibbs' canonical distribution with conserving the time-reversibility. A condition for equations of motion for the system with…

The Nose-Hoover thermostat is a deterministic dynamical system designed for computing phase space integrals for the canonical Gibbs distribution. Newton's equations are modified by coupling an additional reservoir variable to the physical…

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…