About Workshop
This three-day hands-on workshop introduces protein–ligand molecular dynamics simulation using GROMACS in Google Colab. Participants will prepare and equilibrate a validated protein–ligand system, analyse molecular stability and interaction persistence, and interpret MM/PBSA energy components.
The workshop covers RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, residue contacts, protein–ligand distances, and research-ready result interpretation. A validated production trajectory will be provided for practical analysis, enabling participants to complete the workflow within the live workshop duration.
Aim
To provide participants with practical expertise in protein–ligand molecular dynamics simulation using GROMACS and Google Colab, enabling them to prepare simulation systems, analyse molecular stability and protein-ligand interactions, interpret MM/PBSA energy estimates, and generate scientifically reliable results for computational drug discovery and structural biology research.
What Participants Will Learn
- Build a complete protein–ligand molecular dynamics workflow using GROMACS in Google Colab.
- Prepare simulation-ready protein–ligand systems and perform system equilibration.
- Analyse molecular dynamics trajectories using standard structural stability metrics.
- Identify persistent protein–ligand interactions and evaluate binding behaviour.
- Perform and interpret MM/PBSA-based binding energy analysis.
- Present molecular dynamics results through publication-ready plots, tables and scientific summaries for computational drug discovery research.
Structure
Day 1: Protein-Ligand System Preparation and Equilibration
Core Objective: Prepare a validated protein-ligand complex for molecular dynamics simulation and understand the essential stages required before production MD.- Role of molecular dynamics after molecular docking
- Protein-ligand structure inspection and preparation
- Removal of unwanted molecules, alternate conformations, and structural inconsistencies
- Selection of protein force field and compatible water model
- Integration of protein and ligand topology files
- Simulation-box generation, solvation, and ion addition
- Energy minimisation and convergence assessment
- NVT equilibration for temperature stabilisation
- NPT equilibration for pressure and density stabilisation
- Preparation of the equilibrated system for production simulation
Day 2: Molecular Dynamics Trajectory and Stability Analysis
Core Objective: Process a molecular dynamics trajectory and evaluate protein stability, ligand movement, residue flexibility, and structural compactness.- Understanding molecular dynamics trajectory and topology files
- Correction of periodic-boundary-condition artefacts
- Protein centring, molecular reconstruction, and trajectory fitting
- Protein-backbone RMSD for structural stability assessment
- Ligand heavy-atom RMSD after protein alignment
- Residue-level RMSF for identifying flexible protein regions
- Radius of gyration for evaluating protein compactness
- Solvent-accessible surface area analysis
- Protein–ligand centre-of-mass and residue-distance analysis
- Visual inspection of ligand movement within the binding pocket
- Interpretation of stability, fluctuation, and conformational changes
- Common errors in RMSD and trajectory interpretation
Day 3: Interaction Persistence and MM/PBSA Analysis
Core Objective: Identify persistent protein–ligand interactions, interpret MM/PBSA energy components, and prepare an integrated molecular dynamics results summary.- Protein–ligand hydrogen-bond analysis
- Hydrogen-bond occupancy and interaction lifetime
- Residue-wise protein–ligand contact-frequency analysis
- Identification of persistent and transient binding-site interactions
- Preparation of protein–ligand interaction timelines
- Selection of representative trajectory frames
- Principles and workflow of MM/PBSA analysis
- Preparation of receptor and ligand index groups
- Interpretation of van der Waals and electrostatic contributions
- Interpretation of polar and non-polar solvation energies
- Optional per-residue energy decomposition
- Limitations of MM/PBSA and endpoint energy methods
- Integration of docking, MD stability, interaction, and energy results
- Preparation of figures, tables, methods, and research-style conclusions
Important Dates
Registration Ends
3:00 PM
Workshop Dates
2026-08-03
04:00 PM
04:00 PM
What You Will Gain
- Certificate of participation / completion
- Live & recorded sessions
- Post-workshop query support
- Hands-on learning experience.
Outcomes
- Build a complete protein–ligand molecular dynamics workflow using GROMACS in Google Colab.
- Prepare simulation-ready protein–ligand systems and perform system equilibration.
- Analyse molecular dynamics trajectories using standard structural stability metrics.
- Identify persistent protein–ligand interactions and evaluate binding behaviour.
- Perform and interpret MM/PBSA-based binding energy analysis.
- Present molecular dynamics results through publication-ready plots, tables and scientific summaries for computational drug discovery research.
Who Should Attend
PhD scholars working in computational drug discovery, structural bioinformatics or molecular modelling.
Postgraduate students in biotechnology, bioinformatics, pharmacy, biochemistry and life sciences.
Faculty members supervising molecular docking or molecular dynamics projects.
Researchers involved in protein-ligand interaction studies.
Computational biology and cheminformatics learners.
Pharmaceutical and biotechnology professionals.
Researchers preparing dissertations, theses, manuscripts or project reports involving docking and molecular dynamics.
Learners who have completed a molecular docking workshop and want to progress to dynamic protein–ligand analysis.
Deliverables
- Certificate of participation / completion
- Live & recorded sessions
- Post-workshop query support
- Hands-on learning experience.