ABS:Mm gff: Difference between revisions
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*Empirical: can be parameterized from ab initio calculations or experimental data<br> | *Empirical: can be parameterized from ab initio calculations or experimental data<br> | ||
<br> | <br> | ||
[[File:MMFF.png | 580px]] | |||
[[ | |||
<br> | <br> | ||
<math>x^2</math> | |||
<math>U=U_{bonded}+U_{nonbonded}\,</math> | <math>U=U_{bonded}+U_{nonbonded}\,</math> | ||
<math>\sum_{a}^{b}x_{c}</math> | <math>\sum_{a}^{b}x_{c}</math> | ||
= Intermolecular (nonbonded) force | = Intermolecular (nonbonded) force = | ||
'''An excellent mongraph by Stone''' <ref name="stonebook">Stone, A.J., The Theory of Intermolecular Forces. International Series of Monographs on Chemistry. 1996, Oxford: Oxford University Press.</ref><br> | '''An excellent mongraph by Stone''' <ref name="stonebook">Stone, A.J., The Theory of Intermolecular Forces. International Series of Monographs on Chemistry. 1996, Oxford: Oxford University Press.</ref><br> | ||
| Line 35: | Line 33: | ||
</ref> | </ref> | ||
[[File: | [[File:CieplakTable1.png]] | ||
= General force fields = | = General force fields = | ||
Latest revision as of 09:30, 8 May 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
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]
General force fields
- MMx (Allinger)
- AMBER
- CHARMM
- OPLSAA
- GROMOS
- AMOBEA
Software and Documentation
Public MM software with manuals that describe force fields:
- AMBER
- 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 
Mackerrel 2004 [3] 
Cieplak 2009 
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.
- ↑ Stone, A.J., The Theory of Intermolecular Forces. International Series of Monographs on Chemistry. 1996, Oxford: Oxford University Press.
- ↑ 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. -.
- ↑ http://www3.interscience.wiley.com/journal/109086601/abstract?CRETRY=1&SRETRY=0