ffsshhttiikk 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