Introduction #

Find here a growing list of tutorials.

General #

• YouTube channel of the High Performance Computing Center North @ Umeå University, Sweden

  • Best practices for QM/MM

• Best practices in QM/MM simulations of biomolecular systems by the BioExcel Centre of Excellence

• Ensembler is a tool for fast prototyping or teaching principles of molecular simulations. Ensembler is a Python package that can be used directly with Google Colab or installed via PIP (B. Ries, S. Linker, D. F. Hahn, G. König, S. Riniker, JCIM 2021, 61, 2, 560). Check out examples including:

  • Potentials used for Modelling
  • First Simulations
  • Enhanced Sampling Methods:
  • Free Energy Calculations:
  • The Conveyorbelt Integration Scheme (advanced):
  • Enveloping Distribution Sampling (advanced):

Molecular Mechanics #

GROMACS #

• Beginner tutorials series by Justin A. Lemkul, Virginia Tech

  • Setting up simulations
  • Simulation of membrane proteins
  • Umbrella sampling
  • Biphasic systems
  • Protein/ligand interactions
  • Free energy calculations
  • Virtual sites

• GROMACS/cp2k QM/MM MD tutorial series by the BioExcel Centre of Excellence

  • Introduction to QM/MM - First part
  • First Q&A session
  • First practical session
  • Introduction to QM/MM - Second part
  • Second Q&A session
  • Second practical session
  • Introduction to QM/MM - Third part
  • Third Q&A session
  • cp2k parameter special
  • Third practical session

Mixed QM/MM Software #

pDynamo #

• GTKDynamo and EasyHybrid series by Jose Fernando R Bachega
  • Cyclohexane reaction path
  • SN2 reaction - part 1
  • SN2 reaction - part 2
  • My first QC/MM system
  • Building a system using Ambertools
  • Charges per block
  • Enzyme reaction
  • Umbrella sampling

Quantum Mechanics (QM) Software #

ORCA #

• ORCA tutorials series by the makers

PSI4 #

• PSI4 General Tutorial with Python API
• Introduction to DFT

Cheminformatics Software #

General #

• Practical Cheminformatics by Pat Walters
• Is life worth living blog on Cheminformatics

RDKit #

• RDKit Documentation
• The RDKit Cookbook
• Getting started with RDKit in Python
• Getting started with RDKit in C++
• The RDKit Book