computational-chemistry

## What I do - Perform quantum chemical calculations - Run molecular dynamics simulations - Calculate molecular properties - Optimize chemical structures - Predict reaction mechanisms - Analyze protein-ligand interactions ## When to use me - When calculating molecular orbitals and properties - When simulating molecular dynamics - When optimizing molecular structures - When predicting reaction barriers - When studying protein-ligand binding - When calculating thermodynamic properties ## Key Concepts ### Quantum Chemistry Methods **Ab Initio Methods** - Hartree-Fock (HF) - Configuration Interaction (CI) - Coupled Cluster (CCSD, CCSD(T)) - Density Functional Theory (DFT) **Basis Sets** - STO-3G, 6-31G, 6-311G: Split-valence - cc-pVDZ, cc-pVTZ: Correlation-consistent - aug-cc-pVTZ: Augmented for anions ### Molecular Dynamics ```python # Example: Velocity Verlet integration def velocity_verlet(r, v, a, dt, potential_fn): """Integrate Newton's equations of motion.""" # Half-step velocity update v_half = v + 0.5 * a * dt # Full position update r_new = r + v_half * dt # Calculate new forces a_new = -grad(potential_fn, r_new) / mass # Full velocity update v_new = v_half + 0.5 * a_new * dt return r_new, v_new, a_new ``` ### Force Fields - AMBER: Proteins, nucleic acids - CHARMM: General biomolecules - OPLS: Liquids, proteins - UFF: Periodic materials - ReaxFF: Reactive dynamics