Our group does not typically carry out classical molecular dynamics simulations. However, with the advent of machine-learned interatomic potentials, the use of ML-accelerated ab initio molecular dynamics (AIMD) simulations is becoming commonplace for us.
The main tool for classical MD is LAMMPS , but some ML packages do not have an interface to LAMMPS. Instead, most ML interatomic potentials have an interface to ⭐ASE and its molecular dynamics modules . Some codes, like VASP, have built-in routines for ab initio MD as well. - MDAnalysis : Analyze MD simulations.
- mdtraj : Analyze MD trajectories.
- pyscal : Local order parameter analysis.
- Freud : Analysis of environments in trajectories
Don't hesitate to chat with others to learn more about MD. There is plenty of experience in at Princeton in this area. In our department, chat with the students in Prof. Mike Webb's group. Outside the department, Prof. Roberto Car's group knows a lot about AIMD in particular.