Introduction to Molecular Dynamics with GROMACS and CHARMM-GUI
Learn to run real molecular simulations, from a raw PDB file to a published-quality analysis.
About this course
A hands-on, cohort-based course teaching computational science through structured lectures, guided reading, collaborative live laboratories, assignments, and cloud-based research environments. You'll prepare a real protein structure, run it through energy minimization, equilibration, and production molecular dynamics, and analyze the resulting trajectory — the same workflow used in real structural biology research.
Who it's for
Graduate students, advanced undergraduates, and early-career researchers in biology, chemistry, biophysics, or related fields who want hands-on experience with molecular simulation.
Prerequisites
Comfort with basic biology or chemistry concepts. No prior Linux, GROMACS, or programming experience required — we teach these from the ground up.
Learning outcomes
By the end of this course you will be able to prepare a protein structure for simulation, run energy minimization and equilibration, launch and monitor a production molecular dynamics run, and analyze a trajectory to answer a real scientific question.
Weekly structure
Molecular Dynamics Foundations
An introduction to why molecules move, how molecular dynamics simulations work, and the physics underneath them.
Protein Preparation with CHARMM-GUI
Preparing a real protein structure for simulation using CHARMM-GUI's Solution Builder.
GROMACS Files and Energy Minimization
Understanding the core GROMACS file types and running your first energy minimization.
Equilibration
Bringing a minimized system to the correct temperature and pressure before production.
Production Molecular Dynamics
Running, checkpointing, and restarting production simulations.
Trajectory Analysis
Extracting scientific insight from a finished trajectory.
- Duration
- 6 weeks
- Cohort capacity
- 10 students
- Seats remaining
- 10
- Commitment
- Approximately 5–7 hours per week, including one scheduled live laboratory session.
- Certificate
- Included
- Cost
- Free