The tutorials are divided in a set of sections, each containing several guides into several functionalities of HTMD:

  • The first section focuses on teaching the basics of HTMD, ideal for those starting with the software

  • The second section introduces the HTMD tools available to prepare and build systems for MD simulations

  • The third section explains how to setup and run MD simulations using HTMD

  • The fourth section is about analysis of MD simulations using Markov state models

  • The fifth section showcases some advanced uses of HTMD

  • The sixth section contains examples on how to use useful tools included in HTMD

  • The last section is a changelog of the modifications to HTMD along versions