Difference between revisions of "ABS:Mm gff"

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(Created page with "= 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<br> <br> 800px<span class="texhtml"> </span> <br>...")
 
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= Reviews  =
= Reviews  =


Ponder and Case 2003 [[File:ponder-case.pdf| 600px]]
Ponder and Case 2003 [[File:ponder-case.pdf| 300px]]


Mackerrel 2004 <ref> http://www3.interscience.wiley.com/journal/109086601/abstract?CRETRY=1&amp;SRETRY=0 </ref> [[File:Forcefield-review.pdf‎ | 600px]]
Mackerrel 2004 <ref> http://www3.interscience.wiley.com/journal/109086601/abstract?CRETRY=1&amp;SRETRY=0 </ref> [[File:Forcefield-review.pdf‎ | 600px]]


Cieplak 2009 [[File:Cieplak_forceifeld_pol_jpcb2009.pdf | 600px]]
Cieplak 2009 [[File:Cieplak_forceifeld_pol_jpcb2009.pdf | 300px]]
  Most developments in the polarizable force fields for biomolecules
  Most developments in the polarizable force fields for biomolecules
  relate to explicitly induced dipoles and somewhat less to
  relate to explicitly induced dipoles and somewhat less to

Revision as of 16:44, 22 April 2022

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


Forcefield.png



Intermolecular (nonbonded) force

An excellent mongraph by Stone [1]

  • 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 -
    • Damping +

A quantitative comparison:[2]

Cieplak table1.PNG

General force fields

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

Software and Documentation

Public MM software with manuals that describe force fields:

Reviews

Ponder and Case 2003 Ponder-case.pdf

Mackerrel 2004 [3] Forcefield-review.pdf

Cieplak 2009 Cieplak forceifeld pol jpcb2009.pdf

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.
  1. Stone, A.J., The Theory of Intermolecular Forces. International Series of Monographs on Chemistry. 1996, Oxford: Oxford University Press.
  2. Cieplak, P., F.Y. Dupradeau, Y. Duan, and J.M. Wang, Polarization effects in molecular mechanical force fields. Journal of Physics-Condensed Matter, 2009. 21(33): p. -.
  3. http://www3.interscience.wiley.com/journal/109086601/abstract?CRETRY=1&SRETRY=0