Basics questions

  1. What does it indicate when there is a sudden increase in potential energy (or total energy) during a simulation?
  2. How can one identify the suitable simulation steps to apply the energy minimization function, and is it advisable to perform it at multiple stages?
  3. How to verify if a system has achieved equilibrium during a simulation.

It could mean many things I suppose. The ones that come to my mind are (a) a first order phase transition or (b) a simple quick change in energy as the atoms in your system rearrange themselves in space from an initial configuration that was maybe generated randomly.

What do you mean here? Unless you are trying to reach some sort of minimal energy configuration (as opposed to study the many microstates and the corresponding instantaneous values of properties that occur throughout the dynamics), I dont see why you would need to stop your molecular dynamics (MD) simulation to do energy minimizations. If you are trying to mix MD and energy minimizations to reach an initial configuration that is “usable” within MD from a very unstable initial one, I dont think there is a rule to how often you should do energy minimizations.

I think that many people agree there is no ultra-solid way to make the statement “my system equilibrated”, but if the mean value around which instantaneous values of properties fluctuate does not change with time within a reasonable time interval, it is a good indicator that your system has equilibrated.

1 Like