GROMACS: Molecular Dynamics Simulation (MDS)

Description

💻 3-Day Hands-On Workshop | 🕒 1–1.5 Hours/Day

Day 1: Linux Basics & GROMACS Installation

• Introduction to Molecular Dynamics (MD)
• Why GROMACS and Linux for MDS?
• Basic Linux commands: cd, ls, nano, chmod, cp, mv
• Installing GROMACS (via apt, conda, or source)
• Testing GROMACS installation: gmx -h
• Practice: Navigate Linux, install GROMACS, and run a sample test

Day 2: Simulation Setup and Execution

• Preparing input structure: pdb2gmx, force fields, water models
• Box creation & solvation: editconf, solvate
• Adding ions: grompp, genion
• Energy Minimization → NVT → NPT → Production MD
• Commands: gmx grompp, mdrun, .mdp file overview
• Practice: Run a full short simulation pipeline on sample protein

Day 3: Trajectory Analysis & Visualization

• Key analysis commands:
  • RMSD (gmx rms)
  • RMSF (gmx rmsf)
  • Radius of Gyration (Rg) (gmx gyrate)
  • SASA (gmx sasa)
  • Hydrogen Bonds (gmx hbond)
• Graph generation with xmgrace / matplotlib / Excel
• Visualizing MD trajectory using VMD or PyMOL
• Summary: simulation interpretation & next steps
• Q&A + discussion of user problems/projects