Tutorials 2019

Here, we show basic, standard, and advanced MD tutorials using GENESIS version 1.7.1. For version 2.0 or later, see Tutorials 2022. 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. 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

Level 3: Advanced MD tutorials

  1. Replica-exchange molecular dynamics simulation (REMD)
  2. Replica-exchange umbrella sampling (REUS)
  3. Replica-exchange solute tempering (gREST)
  4. Gaussian accelerated MD
  5. Replica path sampling
  6. Free energy perturbation
  7. QM/MM
  8. Cryo-EM flexible fitting
  9. Simulations with recent residue-level coarse-grained models


Old tutorials