computational-chemistry

name	computational-chemistry
description	Computer simulation of chemical systems
license	MIT
compatibility	opencode
metadata	{"audience":"computational chemists, researchers, modelers","category":"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

# 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