Tutorials and Other Documents

GROMACS

• Manuals and Documentation
  • GROMACS User Guide
  • GROMACS Reference Manual
  • GROMACS Short How-To Guides
  • GROMACS Molecular Dynamics Parameters (.mdp Options)
  • BioExcel - GROMACS Training and Support
• Tutorials
  • GROMACS Tutorials - gromacs.org
  • From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package (also available as an LiveCOMS Article)

PLUMED

• Manuals and Documentation
  • PLUMED Manual (v2.9)
  • PLUMED Manual (v2.8)
  • PLUMED-NEST The public repository of the PLUMED consortium
• Tutorials
  • PLUMED Masterclass Tutorials
    Corresponding YouTube videos with lectures and solutions found here
    • Masterclass 21.1: PLUMED syntax and analysis
    • Masterclass 21.2: Statistical errors in MD
    • Masterclass 21.3: Umbrella sampling
    • Masterclass 21.4: Metadynamics
    • Masterclass 21.5: Simulations with multiple replicas
    • Masterclass 21.6: Dimensionality reduction
    • Masterclass 21.7: Optimizing PLUMED performances
    • Masterclass 22.3: OPES method
    • Masterclass 22.11: Variationally enhanced sampling with PLUMED

Python

• Manuals and Documentation
  • Python 3 Documentation
  • NumPy User Guide
  • NumPy API Reference
  • MolSSI – Best Practices
• Tutorials
  • Scientific Computing From Scratch
  • MolSSI – Python Scripting for Computational Molecular Science
  • MolSSI – Best Practices in Python Package Development
  • Software Carpentry – Programming with Python
  • Software Carpentry – Plotting and Programming in Python
  • Think Python, 3rd edition

Scientific Visualization

• Manuals and Documentation
  • Scientific Visualization: Python + Matplotlib (Github Repository)
  • Matplotlib Documentation
  • Matplotlib Cheat Sheets
• Tutorials
  • Matplotlib Tutorials

LaTeX

• Manuals and Documentation
  • Overleaf LaTeX Documentation
• Tutorials
  • Overleaf Learn LaTeX in 30 Minutes

Linux and Bash

• Tutorials
  • Software Carpentry – The Unix Shell
  • Ubuntu – The Linux command line for beginners
• Cheat Sheets
  • Bash cheat sheet

Editors

• Tutorials
  • Learn Vim For the Last Time: A Tutorial and Primer
  • Visual Studio Code - Getting Started

Version Control

• Manuals and Documentations
  • GitHub Git Cheat Sheet
• Tutorials
  • Software Carpentry – Version Control with Git