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
MD Foundations, Time Steps and Simulation Length
Understand how an MD trajectory is generated, calculate simulation length from dt and nsteps, plan output frequency, and prepare SimLab Desktop for the practical workflow.
Building Simulation Systems with CHARMM-GUI and SimLab
Build the same solvated protein system in CHARMM-GUI and SimLab, inspect the generated GROMACS files, and compare scientifically meaningful setup choices.
GROMACS Files and Energy Minimization
Read a GROMACS project, preprocess it safely, minimize poor contacts, and interpret convergence without confusing minimization iterations with physical simulation time.
Equilibration, Temperature and Pressure Control
Understand what equilibration is designed to establish and compare staged NVT/NPT teaching protocols with combined or multi-stage protocols generated by modern builders.
Production Molecular Dynamics
Plan and run production MD with explicit duration, output and restart calculations, then verify that the trajectory matches the intended protocol.
Trajectory Analysis and Scientific Communication
Extract structural measurements with native GROMACS, reproduce one analysis in Python, interpret the results and assemble a concise mini manuscript.
- Duration
- 6 weeks
- Commitment
- Approximately 5–7 hours per week, including one scheduled live laboratory session.
- Certificate
- Included
- Cost
- Free
Cohorts
Cohort 1
33/40 enrolled
Cohort 2
36/40 enrolled
Cohort 3
41/41 enrolled
Cohort 4
164/181 enrolled
No cohort is open for applications right now.