Molecular Dynamics Simulation (Online Hands-on Workshop)

29 April-02 May 2026 | 6:30 PM IST | Online Hands-on Workshop | Certificate

About the Workshop

This online hands-on workshop provides a comprehensive understanding of molecular dynamics (MD) simulations and their applications in drug discovery. Participants will learn how to set up simulations, run them using GROMACS, and analyze results to study protein–ligand interactions and stability.

What You Will Learn

• Fundamentals of molecular dynamics simulation

• Setting up protein–ligand systems

• Simulation parameters (force fields, solvation, temperature, pressure)

• Running MD simulations using GROMACS

• Energy minimization and equilibration

• Trajectory analysis (RMSD, RMSF)

• Binding free energy calculations

• Visualization using PyMOL
  

Course Features

• Live hands-on workshop sessions

• e-Certificate upon completion

• Session recordings for revision

• Software installation support

• Protocols and lecture PPTs provided

Learning Outcomes

• Set up and execute MD simulations independently

• Analyze protein–ligand interactions over time

• Interpret simulation outputs and trajectories

• Apply MD techniques in drug discovery research

• Use computational tools for advanced bioinformatics studies
  

Who Can Join

• Undergraduate and postgraduate students in Life Sciences

• Research scholars and faculty members

• Professionals in Biotechnology, Bioinformatics, and Pharmaceutical sciences

• Medical, Pharmacy, and Chemical Sciences background

  
  Course Fee
  Indian Participants: 1400 INR
  International Participants: 75 USD

  
  Workshop Module
  

  Day 1: Introduction to Molecular Dynamics (MD) Simulation

  • Basics of molecular dynamics and its relevance to drug discovery

  • Setting up MD simulations for protein–ligand complexes

  • Simulation parameters: force fields, solvation models, temperature, pressure, and time steps

  • Hands-on: Using GROMACS to set up a basic MD simulation

  Day 2 & 3: Running MD Simulation

  • Understanding solvation, ionization, energy minimization, equilibration, and production MD run

  • Hands-on: Executing a simulation for a specific protein–ligand complex using GROMACS

  Day 4: Analyzing MD Simulation Results

  • Extracting and interpreting MD trajectories: RMSD, RMSF, and binding free energy calculations

  • Stability assessment of protein–ligand interactions over time

  • Generating and visualizing dynamic trajectories

  • Hands-on: Using PyMOL to analyze MD results