In classical molecular dynamics, simulations are done in the microcanonical ensemble: number of particles, volume, and energy have a constant volume. In experiments, the temperature is generally controlled instead of the energy. The ensemble of this experimental condition is called the canonical ensemble.
Nose-Hoover non-Hamiltonian equations of motion which are designed to generate positions and velocities sampled either the canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) thermostats. Nose-Hoover non-Hamiltonian equations of motion which are designed to generate positions and velocities sampled either the canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) thermostats.
The supercell and shape can change dynamically during an MD simulation to equilibrate the internal stress with externally applied constant stress. In these simualations
A Nose-Hoover themostat will not work well for arbitrary values of Tdamp. If Tdamp is too small, the temperature can fluctuate wildly; if it is too large the temperature will take a long time to equilibriate. A good choice for many models is a Tdamp of around 100 timesteps.