Hi Justin,<br><br>Thanks for the reply and the reference.<br>I knew that I am asking for a broad question. <br>OPLS will work for my protein problem. The reason why I am asking the question is to know how diffirent water models work for OPLS and is there any comparison work done for it. The reference you mentioned helps in some way.<br>
I will read more to teach myself about this broad question.<br><br>Jianhui<br><br>Date: Wed, 13 Apr 2011 15:50:49 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] OPLS with Water models<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DA5FE99.6020204@vt.edu">4DA5FE99.6020204@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Jianhui Tian wrote:<br>
> Hi,<br>
><br>
> This has been a long discussed question. But I am still not so clear<br>
> after reading some posts and papers.<br>
> What model should be used for OPLS-AA force field? Any consideration for<br>
> the choice? Is SPC/E a good one?<br>
><br>
> Michael shirts has said in<br>
> <a href="http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html</a><br>
> "Jorgensen's OPLS-AA (and more recent OPLS-AA/L) force fields were<br>
> developed almost completely with TIP4P water. "<br>
> Also, David van der spoel had a paper with Erik Lindahl (JPCB 2003,<br>
> 117, 11178-11187) confirming: "OPLS works better with TIP4P".<br>
><br>
> However, many simulations using OPLS with SPC or TIP3P.<br>
><br>
> Alan Wilter S. da Silva said in<br>
> <a href="http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.html</a> that<br>
><br>
> "I did short tests with spce and I got a paper with Dr. der Spoel."<br>
> But I can not find any paper for OPLS-AA and SPC/E water.<br>
><br>
> Suggestions or references are welcomed.<br>
<br>
Well, there's this one that endorses SPC/E for several properties:<br>
<br>
<a href="http://dx.doi.org/10.1021/jp0641029" target="_blank">http://dx.doi.org/10.1021/jp0641029</a><br>
<br>
What you've asked is extremely broad. Different force fields and solvent models<br>
can be combined in a number of ways to measure various quantities. It all comes<br>
down to what you're hoping to measure. Is it protein conformational sampling?<br>
Reproducing NMR signals? Hydration energies or other thermodynamic properties?<br>
Then there's the complication of whether or not OPLS-AA is inherently the best<br>
choice to represent your protein for these endeavors. There has been a wealth<br>
of recent literature on force field comparisons for protein dynamics, as well.<br>
<br>
-Justin