Protein–Ligand Molecular Dynamics Research Project
Research mentor:
4.0
Take a protein–ligand complex from raw structure to a finished simulation in GROMACS. You prepare the system, parameterise the ligand, run the dynamics, and come away with your own analysed trajectory and interaction plots.
Explore free modules at no cost to see if this research project matches your learning goals.
Project Objectives
Understand Protein–Ligand MD Simulation
Understand the principles, workflow, and key differences between apo-protein and protein–ligand molecular dynamics simulations.
Prepare and Parameterise the System
Learn to prepare protein and ligand structures, generate ligand parameters, and build a simulation-ready protein–ligand complex.
Perform Molecular Dynamics Simulation
Develop practical skills to set up, minimise, equilibrate, and run protein–ligand MD simulations using GROMACS.
Analyse MD Simulation Results
Perform essential trajectory analyses to evaluate the stability, structural behaviour, and interactions of the protein–ligand complex.