Tutorials

We show basic, intermediate, and advanced tutorials for GENESIS. Before starting the tutorials, the users are recommended to get VMD to visualize the obtained MD trajectories, and also gnuplot to plot the data. We will use various linux commands such as grepcutpastetailsed, and tee. If you do not know their basic usage, learn them in advance. The GENESIS beginners may first start the basic tutorial, which can be mainly performed on a few CPU cores. However, most tutorials at the intermediate and advanced levels require parallel computation with many cores, because their calculations are heavy. The tutorials are mainly composed of three levels according to the required computational resource.

  • : Suitable for laptop or small desktop machine (atdyn, less than 4 CPU cores)
  • : Suitable for workstation or GPU machine (spdyn, ~16 CPU cores)
  • : Suitable for cluster machine or super-computer (spdyn, 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 the all-atom model
  3. MD simulations with the coarse-grained model
  4. MD simulations with the implicit solvent model
  5. MD simulations with various restraints (in preparation)

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

Appendix

Old tutorials