Ammm:Mm gff

Molecular Mechanics

• Atom based: atoms are the basic particles; electron and nuclei information are averaged out
• Classical: atoms interact with each other according to classical force field (or potential energy function)
• Additive: the total energy (Hamiltonian) is a sum of all pair-wise interactions
• Empirical: can be parameterized from ab initio calculations or experimental data
  

$x^{2}$

$U=U_{bonded}+U_{nonbonded}\,$ $\sum _{a}^{b}x_{c}$

Intermolecular (nonbonded) force

An excellent mongraph by Stone

• Long range: U ~ R^-n
  • Electrostatic (permanent charges, dipoles and quadrupoles…) +/-
  • Induction: Permanent and induced -
  • Instantaneous induction: dispersion -
  • Resonance and magnetic +/-
• Short range: U~ exp(-cR)
  • Exchange -
  • Repulsion +
  • Charge transfer -
  • Penetration - (related to multipole expansion and separation of nuc and electrons)
  • Damping +

A quantitative comparison:

General force fields

• MMx (Allinger)
• AMBER
• CHARMM
• OPLSAA
• GROMOS
• AMOBEA

Software and Documentation

Public MM software with manuals that describe force fields:

• AMBER
• CHARMM
• GROMACS
• NAMD
• DL Poly manual: http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/MANUALS/USRMAN3.09.pdf or http://wanglab.bu.edu/DLPOLY2/node82.html
• Moldy manual: ftp://ftp.dl.ac.uk/ccp5/MOLDY/moldy.pdf
• MSI manual is another good source

Reviews

• Ponder and Case 2003, Force Fields for Protein Simulations [( [[1]] )]
• Jing et al 2019 Polarizable force fields for biomolecular simulations: Recent advances and applications [([[2]] )]
• Polarizable force fields for biomolecular modeling 2015 Reviews in Comp Chem V28 [[3]]
• Biomolecular electrostatics and solvation: a computational perspective 2012
• Polarizable force fields for scoring protein–ligand interactions 2012
• A review of physics-based coarse-grained potentials for the simulations of protein structure and dynamics, Xia 2012

Most developments in the polarizable force fields for biomolecules relate to explicitly induced dipoles and somewhat less to fluctuating charge and Drude oscillator methods. New methods have begun to emerge, such as those that go beyond point charge models and describe charge densities via spatial functions.

Ponder and Case 2003

Mackerrel 2004

Cieplak 2009