QM/MM for Biomolecules — Hands-on

Model chemistry in proteins with hybrid accuracy and scale. Learn to partition QM vs MM regions, choose embeddings, set up interfaces between QC engines and MD packages, locate transition states, and compute reaction free-energy profiles with transparent, reproducible outputs.

QM/MM for Biomolecules (Hybrid Quantum–Molecular Mechanics)

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Session Index

Session 1 — Concepts: Partitioning & Embedding Session 2 — Practical Setup: Engines & Interfaces Session 3 — Reaction Paths, Sampling & Analysis Session 4 — Mini Capstone: Mechanism → ΔG Profile

Session 1

Fee: Rs 6300

Concepts: Partitioning & Embedding

Defining QM vs MM regions: chemistry coverage, size and boundaries

Theory

Capping strategies and boundary handling

link atoms (H) pseudobonds frozen MM shells

Embedding choices and charge treatment

mechanical/electrostatic embedding polarizable embedding (overview) charge derivation (RESP/ESP)

Session 2

Fee: Rs 8400

Practical Setup: Engines & Interfaces

Connecting QC and MD codes; file plumbing & units sanity

ORCA/CP2K/Gaussian* AMBER/CHARMM/GROMACS OpenMM ChemShell/pmx (bridges)

Level of theory selection for biomolecular QM regions

DFT (GGA/hybrid) semiempirical (GFN/AM1/PM6) basis sets & dispersion

Equilibration and restraints around the active site

harmonic shells positional restraints

Session 3

Fee: Rs 11200

Reaction Paths, Sampling & Analysis

Locating TS and mapping mechanisms (overview)

constrained scans NEB/string methods IRC (intrinsic reaction coord.)

QM/MM-MD & free energy profiles along a coordinate

umbrella sampling WHAM integration metadynamics (overview)

Uncertainty & robustness checks

window overlap replicates/bootstraps sensitivity to QM region/level

Session 4

Fee: Rs 14000

Mini Capstone: Mechanism → ΔG Profile

Define QM region, map a key step, and assemble a ΔG profile (reaction coordinate)

Theory + Practical

Provenance & reproducibility checklist (inputs, levels, seeds)

protocol YAML scene & figure exports tables & logs bundle

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

QM/MM for Biomolecules Training | Partitioning, Embedding, Engines, Reaction Paths & Free-Energy Profiles

QM/MM for Biomolecules — Hands-on