相关论文: Benchmarking thermostat algorithms in molecular dy…

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…

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…

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 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…

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 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…

With the objective of demonstrating usefulness of thermostats in the study of dynamic critical phenomena in fluids, we present results for transport properties in a binary Lennard-Jones fluid that exhibits liquid-liquid phase transition.…

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…

Nonequilibrium molecular dynamics (NEMD) has been extensively used to study thermal transport at various length scales in many materials. In this method, two local thermostats at different temperatures are used to generate a nonequilibrium…

We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare'…

We show that a recently introduced stochastic thermostat [J. Chem. Phys. 126 (2007) 014101] can be considered as a global version of the Langevin thermostat. We compare the global scheme and the local one (Langevin) from a formal point of…

We reformulate the algorithm of Gr{\o}nbech-Jensen and Farago (GJF) for Langevin dynamics simulations at constant temperature. The GJF algorithm has become increasingly popular in molecular dynamics simulations because it provides robust…

We investigate a binary Lennard-Jones mixture with molecular dynamics simulations. We consider first a system cooled linearly in time with the cooling rate gamma. By varying gamma over almost four decades we study the influence of the…

Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…

Reliable dynamical properties from molecular dynamics simulations require careful control of thermostatting artifacts. We systematically assess how NVE, deterministic thermostats, velocity-rescale dynamics, and stochastic Langevin-type…

A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps, is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as…

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…

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…

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…

We simulate dynamic mechanical analysis experiments for the Kob-Andersen binary Lennard-Jones system. For this, the SLLOD algorithm with time-dependent strain rates is applied to give a sinusoidally varying strain at different densities and…