MD Simulation Workshop

Molecular Dynamics Simulation Workshop

This hands-on workshop introduces the principles and practical application of molecular dynamics (MD) simulations for studying biomolecular systems. Participants will learn how to prepare protein and ligand structures, set up simulations using popular software like GROMACS or AMBER, run MD simulations, and analyze trajectories to understand molecular behavior over time. Designed for beginners and researchers interested in drug design, structural biology, and biophysics, the workshop blends theory with guided exercises to build your skills in MD simulations.

Workshop Highlights:

• Basics of molecular dynamics and force fields

• Preparing biomolecular systems for simulation

• Setting up and running MD simulations

• Trajectory analysis: RMSD, RMSF, hydrogen bonds, and more

• Visualization of dynamic molecular interactions

• Interpretation of simulation results

• Troubleshooting and best practices

Gain hands-on experience to explore molecular flexibility, binding stability, and conformational changes that drive biological function.