Related papers: Constant-temperature molecular-dynamics algorithms…
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird…
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…
Almost all Molecular Dynamics (MD) simulations are discrete dynamics with Newton's algorithm first published in 1687, and much later by L. Verlet in 1967. Discrete Newtonian dynamics has the same qualities as Newton's classical analytic…
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 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…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
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…
Using the isothermal molecular dynamics (MD), coalescence/sintering of Au nanoparticles (NPs) was simulated by employing the Nose-Hoover thermostat. The MD simulation was realized by using the well-known open program LAMMPS, its version for…
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…
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 this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
An extended Hamiltonian approach to conduct isothermal-isobaric molecular dynamics simulations with full cell flexibility is presented. The components of the metric tensor are used as the fictitious degrees of freedom for the cell, thus…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
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…
Ab initio molecular dynamics (AIMD) is a powerful tool to predict properties of molecular and condensed matter systems. The quality of this procedure is based on accurate electronic structure calculations. The development of quantum…
In this work we extend the applicability of the microcanonical ensemble simulation method, originally proposed to study the Ising model (A. H\"uller and M. Pleimling, Int. Journal of Modern Physics C, 13, 947 (2002),…