Jianhui Tian wrote:
Hi,
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
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html
"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:
http://dx.doi.org/10.1021/jp0641029
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
Thanks.
Jianhui
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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