Stability of MD Simulations. In classical MD, the system of interest is propagated forward in discrete integration time steps, ∆t, according to Newton's equations of motion, usually extended with a thermostat and barostat. The value of ∆t is a trade-off between computational efficiency (sampling of the configuration space) and accuracy (energy and momentum conservation). The time step commonly used in atomistic biomolecular simulations is ∆t ≈ 2 fs. Either increasing ∆t or decreasing the particle masses results in larger particle displacements per single time step, that is, in a single unit of computation. In MD simulations, the time step is usually chosen close to the limit of stable time integration to achieve near-optimal sampling.