MD Analysis, Stability, Energetics & Binding Free Energy — Hands-on

Learn how to turn raw molecular dynamics trajectories into decision ready analyses. This module focuses on trajectory handling, stability and flexibility metrics, interaction and energetics analysis, and MM/PBSA style binding free energy workflows so that you can quantify complex stability and binding strength in a reproducible way.

MD Analysis, Stability, Energetics & Binding Free Energy

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Session Index

Session 1 — Trajectory Handling & Quality Checks Session 2 — Stability & Flexibility Metrics Session 3 — Interactions, Energetics & Clustering Session 4 — Mini Capstone: Binding Free Energy Report

Session 1

Fee: Rs 8800

Trajectory Handling & Quality Checks

MD trajectory formats and preprocessing steps

coordinate and topology files removing PBC jumps and imaging fitting and alignment choices

Basic run quality diagnostics vs time

temperature and pressure traces density, energy and volume checks spotting instabilities and artefacts

Region and selection management for analysis

whole protein vs domain selections ligand and binding site groups reference frames and subsets

Session 2

Fee: Rs 11800

Stability & Flexibility Metrics

Global stability measures

RMSD vs time for backbone and ligand radius of gyration and compactness equilibration window identification

Local flexibility and fluctuation analysis

RMSF per residue mapping fluctuations onto structure loop and binding site flexibility

Conformational descriptors and PCA ideas

principal component projections essential dynamics interpretations connecting motions to function

Session 3

Fee: Rs 14800

Interactions, Energetics & Clustering

Protein ligand interaction analysis over time

hydrogen bonds and salt bridges hydrophobic contacts and pi stacking contact maps and interaction fingerprints

Energetic decomposition concepts

Coulomb and Lennard Jones terms per residue energy contributions idea identifying key stabilizing residues

Clustering conformations and representative structures

distance metrics and clustering options picking centroid structures link to docking and further calculations

Session 4

Fee: Rs 18800

Mini Capstone: Binding Free Energy Report

MM PBSA style binding free energy workflow concepts

Theory + Practical

Prepare snapshots, run calculations and interpret results

snapshot selection from equilibrated window per residue decomposition overview understanding uncertainty and limits

Deliverables: MD stability and binding free energy dossier

plots for RMSD, RMSF and interactions binding free energy tables written interpretation and next step guidance

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MD Analysis, Stability, Energetics & Binding Free Energy Training | Trajectory QC, Interactions & MM/PBSA

MD Analysis, Stability, Energetics & Binding Free Energy — Hands-on