Running a simulation#

This section is to be written, but in the meantime we refer to several good tutorials (MD Tutorials, Gromacs tutorials, OpenMM tutorials) discussing the simulation of molecular dynamics, 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.