相关论文: How Thermostats Influence Dynamics Across Time Sca…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
The numerical investigation of the statics and dynamics of systems in nonequilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level…
Thermostats are dynamical equations used to model thermodynamic variables such as temperature and pressure in molecular simulations. For computationally intensive problems such as the simulation of biomolecules, we propose to average over…
Stochastic thermostats based on the Langevin equation, in which a system is coupled to an external heat bath, are popular methods for temperature control in molecular dynamics simulations due to their ergodicity and their ease of…
Advanced thermostats for molecular dynamics are proposed on the base of the rigorous Langevin dynamics. Because the latter accounts for the subsystem-bath interactions in details, the bath anisotropy and nonuniformity are described via the…
We study numerical methods for sampling probability measures in high dimension where the underlying model is only approximately identified with a gradient system. Extended stochastic dynamical methods are discussed which have application to…
We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise…
A systematic comparison was carried out to assess the influence of representative thermostat methods in constant-temperature molecular dynamics simulations. The thermostat schemes considered include the Nos\'e--Hoover thermostat and its…
A thermostat of the Nose-Hoover type, based on relative velocities and a local definition of the temperature, is presented. The thermostat is momentum-conserving and Galilean-invariant, which should make it suitable for use in Dissipative…
The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The…
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon…
We study the convergence to equilibrium of an underdamped Langevin equation that is controlled by a linear feedback force. Specifically, we are interested in sampling the possibly multimodal invariant probability distribution of a Langevin…
We present a new time-dependent Density Functional approach to study the relaxational dynamics of an assembly of interacting particles subject to thermal noise. Starting from the Langevin stochastic equations of motion for the velocities of…
Thermostats are dynamic equations used to model thermodynamic variables in molecular dynamics. The applicability of thermostats is based on the ergodic hypothesis. The most commonly used thermostats are designed according to the…
Monte Carlo sampling for Bayesian posterior inference is a common approach used in machine learning. The Markov Chain Monte Carlo procedures that are used are often discrete-time analogues of associated stochastic differential equations…
A simple deterministic and time reversal invariant type of thermostat is proposed to be used for computer simulations of classical systems. It acts on collisions with the walls of the container exclusively. It maps the incoming and outgoing…
The developing field of stochastic thermodynamics extends concepts of macroscopic thermodynamics such as entropy production and work to the microscopic level of individual trajectories taken by a system through phase space. The scheme…
Dynamic heterogeneity has often been modeled by assuming that a single-particle observable, fluctuating at a molecular scale, is influenced by its coupling to environmental variables fluctuating on a second, perhaps slower, time scale.…