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

Contents:

• Introduction to HTMD
  • Python primer
  • Getting started with HTMD
  • HTMD Molecules
  • Visualization in HTMD
• Building with HTMD
  • Protein preparation
  • Advanced building
  • System building protein-ligand
  • System building protein in Membrane
• Simulations in HTMD
  • Molecular Dynamics in HTMD
  • Adaptive Sampling Explained
  • Adaptive Sampling Tutorial
• Analysis in HTMD
  • Getting Started with Projections
  • Ligand binding analysis
  • Protein folding analysis
  • CXCL12 conformational analysis
• Advanced uses
  • System building Protein-Protein
  • Using docking to initialize positions
  • Equilibration protocol for the mu opioid GPCR
• Tools
  • Maximal Substructural Alignment
  • Sequence Based Alignment
  • FFEvaluate
  • Membrane Builder
• Changelog
  • 1.12.0 (stable) - 2018/03/22
  • 1.10.0 (stable) - 2017/10/25
  • 1.8.0 (stable) - 2017/07/17
  • 1.6.0 (stable) - 2017/03/01