GENESIS Tutorials 2022

Here, we provide basic, standard, and advanced MD tutorials for GENESIS version 2.x.

Before starting, please ensure that tools like VMD, gnuplot, or python libraries like numpy and matplotlib are installed on your computer. These tools are required for visualizing MD trajectories and plotting output data, respectively.

We strongly encourage all users — especially students and early-career researchers — to begin with the “Level 1: Basic Tutorials” and go through all chapters without skipping. After that, you can proceed to “Level 2: Standard MD Tutorials” or “Level 3: Advanced MD Tutorials.”

Important: Even if you plan to skip some Level 1 chapters, please complete at least Chapters 1.1, 2.1, and 2.2. These chapters establish the common directory structure and input files used in many of the later tutorials. Also, note that Chapter 12 assumes that Chapter 3.2 has been completed.

In the chapter list below, you will find icons such as:

• for laptops (≤ 4 CPU cores),
• for workstations (~ 16 CPU cores),
• for supercomputers (≥ 64 CPU cores).

These indicate the computational requirements of each tutorial. While some chapters can be run on a personal laptop, others require more powerful resources such as clusters or supercomputers. Please select tutorials based on your available resources.

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 Gō 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 Gō model for the open-to-close motions of Ribose Binding Protein
  • 7.4 All-atom Gō 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 longertime 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