Running a simulation

This section is to be written, but in the meantime we refer to several good MD tutorials discussing the simulation of molecular dynamics (including from Justin Lemkul, MolSSI, Compute Canada’s Molecular Modelling and Simulation Team, and program-specific for Gromacs and OpenMM), different software packages for analysis (MDAnalysis, MDTraj), and the wealth of software packages developed for the purpose. We will here primarily make use of the functionalities available in OpenMM, as well as some recent work on Gromacs, and we note that force-field free dynamics can be run with xTB.