Advanced Sampling, Metadynamics, Umbrella & Replica — Hands-on

Go beyond straightforward MD and learn how to map free-energy landscapes, cross barriers and sample rare events in biomolecular systems. This module covers reaction coordinates, metadynamics, umbrella sampling, replica-exchange concepts and practical workflows so that you can design and interpret advanced sampling simulations for real research problems.

Advanced Sampling, Metadynamics, Umbrella & Replica

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Session Index

Session 1 — Free Energy Landscapes & Reaction Coordinates Session 2 — Metadynamics Concepts & Setup Session 3 — Umbrella Sampling, Windows & PMF Session 4 — Mini Capstone: Replica & Advanced Campaign

Session 1

Fee: Rs 8800

Free Energy Landscapes & Reaction Coordinates

Why advanced sampling is needed beyond standard MD

rare events and high barriers metastable states and slow modes connection to kinetics and thermodynamics

Free-energy surfaces and collective variables (CVs)

1D vs 2D free-energy profiles distance, angle and RMSD based CVs choosing CVs aligned with mechanism

Assessing CV quality and basic projection ideas

orthogonality and degeneracy issues connection to PCA and slow coordinates sanity checks using short MD runs

Session 2

Fee: Rs 11800

Metadynamics Concepts & Setup

Metadynamics basics and biasing along CVs

history dependent bias potentials Gaussian height, width and stride ordinary vs well tempered metadynamics idea

Practical metadynamics parameter choices

choosing bias factor and temperature boundary handling and wall potentials avoiding runaway bias and artefacts

Reconstructing free-energy surfaces from metadynamics

accumulated bias and FES reconstruction monitoring convergence indicators interpreting barriers and minima

Session 3

Fee: Rs 14800

Umbrella Sampling, Windows & PMF

Umbrella sampling concepts along a chosen coordinate

harmonic restraints and windows initial structures and pulling runs coverage and overlap requirements

Running umbrella windows and checking sampling quality

histogram overlap checks equilibration vs production frames in each window troubleshooting poorly sampled regions

PMF reconstruction and barrier interpretation

WHAM style reconstruction overview error estimation and confidence bands relating PMF to binding or transition mechanisms

Session 4

Fee: Rs 18800

Mini Capstone: Replica & Advanced Campaign

Replica-exchange ideas and temperature/hamiltonian ladders

Theory + Practical

Design a small advanced sampling campaign for a case system

choosing CVs and method (meta or umbrella) optional replica or multiple walkers concept running and monitoring a short pilot campaign

Deliverables: FES/PMF plots and advanced sampling report

free-energy landscape or PMF profiles parameter tables and convergence diagnostics written interpretation and limitations discussion

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Advanced Sampling, Metadynamics, Umbrella & Replica Training | Free Energy Landscapes & Rare Events

Advanced Sampling, Metadynamics, Umbrella & Replica — Hands-on