GENESIS

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
   • 1.1 Installation of GENESIS for Tutorials
   • 1.2 Let’s take a quick look at the source code of GENESIS
2. Preparation of the input files for GENESIS
   • 2.1 3D structure of biological molecules
   • 2.2 Force field parameters of biological molecules
   • 2.3 Building the initial structure for MD simulation
     
3. MD simulations of peptides and proteins with the all-atom CHARMM force field
   • 3.1 Ala-dipeptide in the gas-phase
     
   • 3.2 (Ala)₃ in water
     
   • 3.3 Protein G in NaCl solution
     
4. Analysis of the MD trajectories
   • 4.1 Analysis of DCD file by the user’s Fortran programming
   • 4.2 Statistical analysis of the trajectory data by Awk
   • 4.3 Statistical analysis of the trajectory data by Python
   • 4.4 How to make a simulation movie with PyMol?

Level 2: Standard MD tutorials

5. Preparation of the input files for various systems
   • 5.1 Creating input files of MD simulations with the CHARMM force field
   • 5.2 Creating input files of MD simulations with the AMBER force field
   • 5.3 Creating input files of MD simulations using the Gromacs input files
     
6. MD simulations of various biomolecules with all-atom models
   • 6.1 POPC lipid bilayer
   • 6.2 GPCR in a lipid bilayer
   • 6.3 N-glycan in water
   • 6.4 RNA in water
7. MD simulations with the coarse-grained model
   • 7.1 Karanicolas-Brooks Go model for the folding simulations of Protein-G
     
   • 7.2 Domain Motion Enhanced model (DoME) for the domain closure of Ribose Binding Protein
   • 7.3 Dual-basin Go model for the open-to-close motions of Ribose Binding Protein
   • 7.4 All-atom Go model for the molten globule simulation of RNase-H protein 
8. MD simulations with the implicit solvent model
   • 8.1 Protein G in the GB/SA model
   • 8.2 Translocator protein (TSPO) in the implicit membrane model
9. MD simulations with various restraints
   • 9.1 Target MD and steered MD simulations of Ribose Binding Protein in water
   • 9.2 Restraint in the NPT ensemble

Level 3: Advanced MD tutorials

10. Atomistic MD simulations using supercomputers and GPU clusters
    • 10.1 Acceleration of MD simulations using HMR and a longer time step
11. Advanced MD simulations with the coarse-grained model
    • 11.1 Coarse-grained simulation of protein with AICG2+ model 
    • 11.2 Coarse-grained simulation of double-stranded DNA with 3PSC.N model 
    • 11.3 Coarse-grained simulation of protein-DNA interactions with PWMcos model 
    • 11.4 Coarse-grained simulation of FUS condensation with HPS model
12. Enhanced conformational sampling simulations of (Ala)₃ in water
    • 12.1 Replica-exchange molecular dynamics (REMD)
      
    • 12.2 Replica-exchange umbrella sampling (REUS)
      
    • 12.3 Replica exchange with solute tempering (gREST)
      
    • 12.4 Gaussian accelerated MD (GaMD)
      
    • 12.5 Gaussian accelerated replica-exchange umbrella sampling (GaREUS)
13. Transition path sampling of biomolecules
    • 13.1 The mean-force string method simulations of (Ala)₃ in water
      
    • 13.2 The closed-to-open motions of Ribose Binding Protein (RBP) with the mean-force string method
14. Free energy perturbations
    
    • 14.1 Relative solvation free energy
      
    • 14.2 Absolute solvation free energy
    • 14.3 Relative protein-ligand binding affinity
15. QM/MM calculations
    • 15.1 What is QM/MM?
    • 15.2 My first QM/MM job 
    • 15.3 How to create a cluster system
    • 15.4 Vibrational analysis of phosphate ion in solution
    • 15.5 The enzyme reaction 1: Reaction path search
    • 15.6 The enzyme reaction 2: Free-energy calculation
16. Experimental data-driven simulations
    • 16.1 Cryo-EM flexible fitting for TPC2 channel
    • 16.2 Cryo-EM flexible fitting with a multi-scale protocol
    • 16.3 Cryo-EM flexible fitting refinement for de novo models 

Appendix

• How to analyze multiple DCD files in the trajectory analysis tools?
• Atomistic MD simulations of biomolecules on GPU clusters
• Atomistic MD simulations of biomolecules on Fugaku
• REMD of protein G with implicit solvent or CG models
• Automatic parameter tuning for REMD, REUS, REST
  
• Removing ring penetrations and chirality errors

Old tutorials

• Tutorials for ver. 1.4-1.6
• Tutorials for ver. 1.0-1.3