Related papers: Advanced Thermostats for Molecular Dynamics
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 Langevin equation accounts for unresolved bath degrees of freedom driving the system toward the bath temperature. Because of this, numerical solutions of the Langevin equation have a long history. Here, we recapitulate, combine, and…
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…
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…
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 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 present in detail a Langevin formalism for constructing stochastic dynamical equations for active-matter systems coupled to a thermal bath. We apply the formalism to clarify issues of principle regarding the sources and signatures of…
When the motion of a probe strongly disturbs the thermal equilibrium of the solvent or bath, the nonlinear response of the latter must enter the probe's effective evolution equation. We derive that induced stochastic dynamics using second…
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…
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 investigate dynamics of a small quantum system open to a bath with thermostat. We introduce another bath, called super bath, weakly coupled with the bath to provide it with thermostat, which has either the Lindblad or Redfield type. We…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
Dynamics of coarse-grained particle systems derived via the Mori-Zwanzig projection formalism commonly take the form of a (generalized) Langevin equation with configuration-dependent friction and diffusion tensors. In this article, we…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
We investigate the dynamics of a massive tracer particle coupled to an interacting active bath, modeled as a harmonic chain of overdamped active particles analytically, with an aim to understand the impact of bath interactions and activity…
We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of…
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…
We study the dynamical behaviour of mesoscopic systems in contact with a thermal bath, described either via a non-linear Langevin equation at the trajectory level -- or the corresponding Fokker-Planck equation for the probability…
Complex environments, such as molecular matrices and biological material, play a fundamental role in many important dynamic processes in condensed phases. Because it is extremely difficult to conduct full quantum dynamics simulations on…
A rigorous two-thermostat formulation for ab-initio molecular dynamics using the fictitious Lagrangian approach is presented. It integrates the concepts of mass renormalization and temperature control for the wave functions. The new…