Enhanced Sampling II: Metadynamics
Map full free energy landscapes with well-tempered metadynamics and PLUMED.
About this course
A hands-on follow-on to Introduction to Molecular Dynamics covering metadynamics, one of the most widely used enhanced sampling techniques in modern computational structural biology. Using PLUMED with GROMACS and alanine dipeptide as the model system, you'll run standard and well-tempered metadynamics, learn to rigorously assess convergence, reconstruct 2D free energy surfaces, and finish with a capstone comparing metadynamics against the other enhanced sampling methods covered across this program.
Who it's for
Graduates of Introduction to Molecular Dynamics (or anyone who passes its qualifying exam) who want to learn metadynamics, one of the most widely used and powerful enhanced sampling techniques in modern MD research. No prior enhanced sampling coursework is required - this course stands on its own.
Prerequisites
Requires Introduction to Molecular Dynamics with GROMACS and CHARMM-GUI - OR solid prior background and hands-on practical experience with MD simulation using GROMACS, proven by scoring at least 85% on the qualifying exam.
Either of the following qualifies you:
- Completed Introduction to Molecular Dynamics with GROMACS and CHARMM-GUI
- Or: solid prior background and hands-on experience with MD simulation using GROMACS, proven by scoring at least 85% on the qualifying exam
Learning outcomes
By the end of this course you will be able to define collective variables and run metadynamics with PLUMED, explain and configure well-tempered metadynamics, rigorously assess convergence via block analysis, reconstruct and interpret 2D free energy surfaces, and make a reasoned, defensible choice between enhanced sampling methods for a new problem.
Weekly structure
Metadynamics Theory and PLUMED Fundamentals
How metadynamics fills free energy wells with a history-dependent bias to drive exploration, and setting up PLUMED with GROMACS to define collective variables.
Well-Tempered Metadynamics
Why standard metadynamics tends to overfill and become unstable at long times, and how well-tempered metadynamics fixes this with a bias factor that tapers hill height over time.
Convergence Diagnostics and Free Energy Surface Reconstruction
Determining whether a metadynamics run has actually converged, and reconstructing the free energy surface from accumulated hills.
Capstone: Comparing Enhanced Sampling Methods
Bringing together everything from this course - and, where applicable, the broader enhanced sampling sequence - into a final capstone comparing metadynamics against the other methods covered in this program.
- Duration
- 4 weeks
- Commitment
- Approximately 5–7 hours per week, including one scheduled live laboratory session.
- Certificate
- Included
- Cost
- Free
Cohorts
No cohort has been scheduled yet.
No cohort is open for applications right now.