Enhanced Sampling: Metadynamics & Replica Exchange — Hands-on

Go beyond classical molecular dynamics and learn how to sample rare events and complex conformational changes using enhanced sampling methods. This module introduces collective variables, free energy landscapes, metadynamics and replica exchange so that you can design, run and interpret enhanced sampling simulations for challenging structural biology and drug discovery questions.

Enhanced Sampling: Metadynamics & Replica Exchange

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Session Index

Session 1 — Rare Events, CVs & Enhanced Sampling Concepts Session 2 — Metadynamics & Free Energy Surface Reconstruction Session 3 — Replica Exchange MD (REMD) Design & Analysis Session 4 — Best Practices, Diagnostics & Case Study

Session 1

Fee: Rs 8800

Rare Events, CVs & Enhanced Sampling Concepts

Limitations of standard MD for rare events

barriers and timescale separation metastable states and slow transitions why enhanced sampling is needed

Collective variables and reaction coordinates

distances, angles and dihedrals path based and multi dimensional CVs choosing CVs for a given process

Overview of enhanced sampling families

metadynamics concepts replica exchange and temperature based methods umbrella and biasing approaches overview

Session 2

Fee: Rs 11800

Metadynamics & Free Energy Surface Reconstruction

Bias potentials and hill deposition

standard metadynamics idea well tempered metadynamics intuition bias factor and hill parameters

Setting up metadynamics simulations

choosing CVs and ranges frequency and height of hills practical coupling to MD engines

Reconstructing and analysing free energy surfaces

FES reconstruction from bias identifying basins and barriers projecting FES onto structural views

Session 3

Fee: Rs 14800

Replica Exchange MD (REMD) Design & Analysis

Principles of replica exchange simulations

independent replicas concept Metropolis exchange criterion temperature vs Hamiltonian REMD

Designing temperature ladders and replicas

choosing number of replicas spacing for target exchange rates balancing cost and efficiency

Analysing REMD trajectories and exchanges

exchange acceptance profiles walking in temperature space reconstructing ensembles at target temperature

Session 4

Fee: Rs 18800

Best Practices, Diagnostics & Case Study

End to end enhanced sampling case study

Theory + Practical

Diagnostics and common pitfalls in enhanced sampling

checking convergence of FES detecting bias artefacts and drift interpreting limited sampling honestly

Connecting enhanced sampling results to projects

using FES for mechanism hypotheses linking barriers to kinetics intuition figures and methods text for reports and papers

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Enhanced Sampling: Metadynamics & Replica Exchange Training | Rare Events & Free Energy Landscapes

Enhanced Sampling: Metadynamics & Replica Exchange — Hands-on