[gmx-users] OPLS with Water models

[Justin A. Lemkul]

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
> 
> 
> 
> 
> 
> 

-- 
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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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