User Guide¶

The user guide is divided in a set of sections, each containing several tutorial-like guides into HTMD several functionalities:

  • 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