[gmx-users] OPLS with Water models

[Jianhui Tian]

Hi Justin,

Thanks for the reply and the reference.
I knew that I am asking for a broad question.
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.
I will read more to teach myself about this broad question.

Jianhui

Date: Wed, 13 Apr 2011 15:50:49 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] OPLS with Water models
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DA5FE99.6020204 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



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.htmlthat
>
> "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
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