Free Energy Calculations & Binding Affinity — Hands-on

From quick end-state estimates to rigorous alchemical workflows: set up, run, and analyze binding free energy calculations with best practices for convergence, uncertainty, and transparent reporting.

Free Energy Calculations & Binding Affinity (MM-PBSA, FEP)

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Session Index

Session 1 — MM-PBSA/GBSA: Theory & Setup Session 2 — Alchemical FEP/TI Workflows Session 3 — Convergence, Errors & Enhanced Sampling Session 4 — Mini Capstone: Affinity Report

Session 1

Fee: Rs 6300

MM-PBSA/GBSA: Theory & Setup

End-state methods, dielectric models and entropy options

Theory

Running MM-PBSA/GBSA on MD snapshots

gmx_MMPBSA MMPBSA.py (AMBER) trajectory subsampling

Interpreting components & sanity checks

ΔE_MM, ΔG_solv, TΔS per-residue decomposition

Session 2

Fee: Rs 8400

Alchemical FEP/TI Workflows

λ-schedules, soft-core potentials, restraints & standard states

Boresch restraints standard-state correction decoupling schemes

Tooling & engines (overview)

GROMACS+PLUMED OpenMM/pmx AMBER TI FEP+*

Analysis: TI/BAR/MBAR and error propagation

BAR/MBAR overlap matrices CI/bootstraps

Session 3

Fee: Rs 11200

Convergence, Errors & Enhanced Sampling

Convergence diagnostics & window overlap checks

time-series decorrelation effective sample size replicates

Umbrella sampling & PMF with WHAM

reaction coordinates biasing & windows WHAM

Enhanced sampling (overview)

REST2/HREX metadynamics (PLUMED)

Session 4

Fee: Rs 14000

Mini Capstone: Affinity Report

Compute ΔG with MM-PBSA and a small FEP/TI example; compare vs literature

Theory + Practical

Uncertainties, convergence plots & reproducibility checklist

BAR/MBAR tables overlap matrices protocol YAML/inputs

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Free Energy Calculations & Binding Affinity Training | MM-PBSA/GBSA, Alchemical FEP/TI, WHAM/PMF, Uncertainty

Free Energy Calculations & Binding Affinity — Hands-on