Tutorials 2022

Here, we show basic, standard, and advanced MD tutorials using GENESIS version 2.0. For version 1.7.1, see Tutorials 2019. Before starting the tutorials, please install VMD and gnuplot in your computer, which will be used for visualizing MD trajectories and plotting output data, respectively. All readers, especially students and young postdocs, are encouraged to first study all chapters in the “Level 1 Basic tutorials” without skipping any chapter, and then go to the “Level 2 Standard MD tutorials” or “Level 3 Advanced MD tutorials”. Even if you really want to skip the Level 1 tutorials, please complete at least Chapters 1.1, 2.1, and 2.2 before going to the next Level tutorials, because common directory structure and common input files created in these chapters are used in the other chapters. Note that Chapter 12 assumes that Chapter 3.2 has been completed. In the following chapter lists, you will find some symbols like , , and , which means laptop, workstation, and super-computer, respectively. In fact, some chapters have low computational costs, while others require supercomputers or cluster machines. Please use reasonable resources or select suitable chapters.

  • : Suitable for laptop or small desktop machine (less than 4 CPU cores)
  • : Suitable for typical Linux workstation (~16 CPU cores)
  • : Suitable for cluster machine or super-computer (more than 64 CPU cores)

Level 1: Basic tutorials

  1. Getting started
  2. Preparation of the input files for GENESIS
  3. MD simulations of peptides and proteins with the all-atom CHARMM force field
  4. Analysis of the MD trajectories

Level 2: Standard MD tutorials

  1. Preparation of the input files for various systems
  2. MD simulations of various biomolecules with all-atom models
  3. MD simulations with the coarse-grained model
  4. MD simulations with the implicit solvent model
  5. MD simulations with various restraints

Level 3: Advanced MD tutorials

  1. Atomistic MD simulations using supercomputers and GPU clusters
  2. Advanced MD simulations with the coarse-grained model
  3. Enhanced conformational sampling simulations of (Ala)3 in water
  4. Transition path sampling of biomolecules
  5. Free energy perturbations (not available in ver 2.0 currently, see Tutorials 2019)
    • 14.1 Relative solvation free energy (in preparation)
    • 14.2 Absolute solvation free energy (in preparation)
    • 14.3 Relative protein-ligand binding affinity (in preparation)
  6. QM/MM calculations
  7. Experimental data-driven simulations

Appendix

Old tutorials