[gmx-users] OPLS with Water models
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 13 21:50:49 CEST 2011
Jianhui Tian wrote:
> This has been a long discussed question. But I am still not so clear
> after reading some posts and papers.
> What model should be used for OPLS-AA force field? Any consideration for
> the choice? Is SPC/E a good one?
> Michael shirts has said in
> "Jorgensen's OPLS-AA (and more recent OPLS-AA/L) force fields were
> developed almost completely with TIP4P water. "
> Also, David van der spoel had a paper with Erik Lindahl (JPCB 2003,
> 117, 11178-11187) confirming: "OPLS works better with TIP4P".
> However, many simulations using OPLS with SPC or TIP3P.
> Alan Wilter S. da Silva said in
> http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.html that
> "I did short tests with spce and I got a paper with Dr. der Spoel."
> But I can not find any paper for OPLS-AA and SPC/E water.
> Suggestions or references are welcomed.
Well, there's this one that endorses SPC/E for several properties:
What you've asked is extremely broad. Different force fields and solvent models
can be combined in a number of ways to measure various quantities. It all comes
down to what you're hoping to measure. Is it protein conformational sampling?
Reproducing NMR signals? Hydration energies or other thermodynamic properties?
Then there's the complication of whether or not OPLS-AA is inherently the best
choice to represent your protein for these endeavors. There has been a wealth
of recent literature on force field comparisons for protein dynamics, as well.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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