Overview
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.
Simulation Tools
The main tool for classical MD is LAMMPS , but most 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. Analysis Tools
mdtraj : Analyze MD trajectories. pyscal : Local order parameter analysis. Freud : Analysis of environments in trajectories