Chapter 14: Classical Force Fields and Water Models

Question 1

Force Fields

Answer 1

• pair potentials help with runtime scaling O(N ²) → O(N )
• more complex systems (e.g. DNA) require more interactions

Question 2

Parameterization of Force Field

Answer 2

• compare to experimental or post-HF results
  
  • can do for coarse-grained particles (e.g. DNA base pairs instead of atoms)
• bond length, angles, force constants
  
  • QM, x-ray crystallography, IR spectroscopy
• dihedral
  
  • QM
• partial charge, LJ constants
  
  • QM, x-ray crystallography

Question 3

Explicit Water Models

Answer 3

• Types
  
  • rigid:
    
    • fixed atomic positions
    • only includes non-bonded interactions
  • flexibile:
    
    • atoms on “springs”
    • includes bond stretching and angle bending
    • produces vibration spectra
  • polarizable:
    
    • include explicit polarization term
    • good for reproducing different phases
• force fields are parameterized for specific water models

Question 4

SPC Model

Answer 4

• simple point-charge model
• rigid model
  
  • only non-bonded interactions
• NOTE: can vary number, location, size and partial charge of interaction sites

Question 5

SPC/E Model

Answer 5

• extended simple point-charge model
• includes average polarization energy
  
  • constant correction E_pol = 1.25 kcal/mol
• results in better diffusion and density than SPC

Question 6

Implicit Water Models

Answer 6

water molecules are modeled as background medium

• Solvent Accessible Surface Area Model:
  
  • determine solvation free energy difference by rolling imaginary sphere around molecule to determine effective interaction surface area for water molecules
• Continuous Electrostatuc Model:
  
  • define spatially dependent dielectric constant ϵ = ϵ(r ) for water
    
    • use in Coulomb interaction