computational-chemistry - SKILL.md Agent Skill

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