Talk:Force field (chemistry)

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Second-generation forcefields[edit]

Can anyone explain what is the difference between the "first" and the "second"-generation force fields? In my opinion, there are no fundamental differences.Biophys 17:59, 2 November 2006 (UTC)[reply]

What are the common features of the "second"-generation force fields? Why these force fields are grouped together? Biohuang (talk) 08:00, 14 February 2014 (UTC)[reply]

The text book "Molecular Modelling: Principles and Applications (2e)" by A. R. Leach mentions class 1, class 2, and class 3 force fields. Class 2 force fields involve "cross-terms" that describe coupling of different internal variables, such as angles and bond lengths, while class 3 force fields have even quantum mechanic terms. I guess 2-generation means class 2 force fields. Biohuang (talk) 02:19, 5 March 2014 (UTC)[reply]

Empirical scoring functions[edit]

There are numerous "statistical" and other empirical scoring functions that are applied for ligand docking, modeling of protein folding, or protein design. An example of those are functions implemented in Rosetta@home. These functions are usually treated as something different from force fields in chemistry. But I am not so sure. They also often implement 6-12 potentials and represent potential energy in a certain approximation (but all force fields are approximate). Still, such functions probably need a separate Wikipedia article. Any opinions?Biophys 17:59, 2 November 2006 (UTC) Empirical scoring functions are different from force field. They do not give you necessarily an energy, which restrict their applications to the ranking of protein-ligand complexes, but they can not be used for thermodynamic properties. However, their are existing empirical scoring functions, which calculate the energy of the complexes. —Preceding unsigned comment added by 212.123.91.18 (talk) 13:27, 18 August 2008 (UTC)[reply]

Forcefield or force field?[edit]

This is usually "force field", for example in the Encyclopedia of Computational Chemistry.Biophys 19:11, 2 November 2006 (UTC)[reply]

Deficiencies[edit]

I wrote new version of Deficiencies section. Feel free to edit minor things. If there are significant questions or disagreements, please let me know here. This is a complicated question that may need a serious discussion. I wrote this based on my protein modeling experience. Biophys 02:28, 3 November 2006 (UTC) I remember a theoreticain saying that force fields in Chemistry are as rigorous as Schrödinger equation because they are based on Laws of Physics (at a seminar). He was corrected by one of his colleagues who happend to be an experimentalist. Biophys 18:10, 6 November 2006 (UTC)[reply]

Is EVB a force field?[edit]

To consider EVB theory as part of force field calculations seems quite strange. At least VB-theory was developed as early as 1928 by Linus Pauling and is considered as molecular orbital theory (see page Valence Bond Theory). As far as I understand the EVB-thoery set up an Hamiltion and the result of solving the equations give a wave function. These are typical characteristics of molecular orbital theory. —Preceding unsigned comment added by 212.123.91.18 (talk) 13:58, 18 August 2008 (UTC)[reply]

A question[edit]

Someone included the following text some time ago (it is removed in current version):

However, the above view seems to overlook the need for free energy calculations and the fact that there is an enormous compensation due to solvation effects and entropic effect that lead to the final small interaction energies ^[1]. Proper force fields with parameters that approximate the correct quantum mechanical interaction energies (including three-body effects, which are modeled in polarizable force fields) should reproduce quite accurately the observed free energies of interaction once the calculations are done with the complex solute/solvent system and with proper free energy calculations.

Please explain what you wanted to tell. Thanks.Biophys (talk) 14:36, 23 April 2009 (UTC)[reply]

What I mean is this. "the fact that there is an enormous compensation due to solvation effects and entropic effect that lead to the final small interaction energies ". True, but this is actually one of several important reasons why molecular mechanics can not reproduce the required small free energy difference. We are dealing with subtraction of huge numbers (thousands of kcal/mol) calculated with inevitable errors to produce very small differences (several kcal/mol). Hence, the errors in calculation of small differences exceed the differences themselves. There was an article by Galaktionov about this; maybe there are other publications.Biophys (talk) 14:52, 23 April 2009 (UTC)[reply]

References

^ Schutz CN. and Warshel A. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44: 400-417.

Spring constant[edit]

"The typical parameter set includes values corresponding to the effective spring constant for each potential" (Parametrization section) Can any body explain it more? —Preceding unsigned comment added by Phoenixinsilico (talk • contribs) 07:46, 3 July 2010 (UTC)[reply]

Distinction from usage in other fields[edit]

As this article appears currently, after Origin2000's edit, there is an, ahem, forceful description of the difference in usage of this term in physics and in chemistry/biophysics. While it's true that this distinction is confusing, please see the neutral point of view policy for why this is inappropriate. The two usages are already disambiguated by the (physics) and (chemistry) labels and both articles carry a hatnote directing users to the force field disambiguation page. Wikipedia articles are not for editorializing and the first sentence of an article is not the place for sharing a personal opinion about the topic. The fact that usages of the term have diverged over time does not make one usage "wrong"; it only necessitates careful explanation of the differences. Opabinia regalis (talk) 05:59, 27 February 2015 (UTC)[reply]

Revised version: explicating the distinction is fine, insulting the field is not. Opabinia regalis (talk) 06:02, 27 February 2015 (UTC)[reply]

Yes, absolutely. There is already a disambig. page. Not only this is confusing, but simply wrong and WP:OR (for example statements like "For this reason, the usage of term force field to define an interatomic potential is indeed wrong."). Reverted. My very best wishes (talk) 03:16, 11 March 2015 (UTC)[reply]

---You are providing a rethorical explaination to something still wrong. Chemistry uses physical concepts for its definitions. Interatomic potential is no exception. Educating people to keep calling an interatomic potential a force field is just unacceptable. That is my personal opinion.

Now, where's the physics in your reply? You are talking about a concept in physics, so you are expected to provide physical formulas if any, rather than rethorics. — Preceding unsigned comment added by Origin2000 (talk • contribs) 08:18, 27 February 2015 (UTC)[reply]

Actually, I'm here on the force field (chemistry) talk page to talk about a concept in chemistry. Physics is thataway if that's the topic you're interested in. This issue is not about "accuracy", it's about terminology. It's not wrong that "chips" are different things in London and New York. Wikipedia exists to report on the literature, not to correct it; the usage described in this article is very well-attested in the literature and if you find it unacceptable you're welcome to take it up with last year's Nobelists Martin Karplus, Arieh Warshel, and Michael Levitt who pioneered the field.

Your edit is not a neutral point of view. This is still editorializing. No adjectives, no adverbs, no opinions, no using Wikipedia to set the record straight. Opabinia regalis (talk) 07:46, 28 February 2015 (UTC)[reply]

@Opabinia. Yes, this must be fixed. Done. My very best wishes (talk) 20:31, 10 March 2015 (UTC)[reply]

Ah, I forgot to get back to this. Origin, I'm glad you found my last edit acceptable but that was just a starting point that removed the disparaging language in the lead. MVBW, thanks for your improvements here. Opabinia regalis (talk) 07:57, 12 March 2015 (UTC)[reply]

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[Shultz-1] Schutz CN. and Warshel A. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44: 400-417.

[1]