Related papers: Isothermal-isobaric molecular dynamics using stoch…
This paper presents a molecular dynamics simulation of an inelastic gas, where collisions between molecules are characterized by a coefficient of restitution less than unity. The simulation employs an event-driven algorithm to efficiently…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and principal thermodynamic properties of a model solution consisting of NaCl salt dissolved in methanol solvent. Four united atom force fields…
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…
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…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
The selection of an equilibrium state by maximising the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of…
Dynamical equations describing physical systems at statistical equilibrium are commonly extended by mathematical tools called "thermostats". These tools are designed for sampling ensembles of statistical mechanics. We propose a dynamic…
A major goal of stochastic thermodynamics is to estimate the inevitable dissipation that accompanies particular observable phenomena in an otherwise not fully accessible system. Quantitative results are often formulated as lower bounds on…
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…
Considerable research has led to ergodic isothermal dynamics which can replicate Gibbs' canonical distribution for simple ( small ) dynamical problems. Adding one or two thermostat forces to the Hamiltonian motion equations can give an…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…
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"…
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…
Stochastic thermodynamics lays down a broad framework to revisit the venerable concepts of heat, work and entropy production for individual stochastic trajectories of mesoscopic systems. Remarkably, this approach, relying on stochastic…
We introduce a description of the collective transverse dynamics of charged (proton) beams in the stability regime by suitable classical stochastic fluctuations. In this scheme, the collective beam dynamics is described by time--reversal…
Usual approach to investigate the statistical properties of deterministically thermostated systems is to analyze the regime of the system motion. In this work the cumulant analysis is used to study the properties of the stationary…
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
We develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric-isothermal ensemble. The viscosity of the liquid increases with pressure,…