[gmx-users] Using TIP4P(2005) with GROMOS-53a6

[João M. Damas]

Furthermore, G53a6 (even with SPC) is problematic for helices in proteins.
I would advise you to use the more recent G54a7.

João

On Mon, Sep 14, 2015 at 3:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/14/15 10:05 AM, Pallavi Banerjee wrote:
>
>> Thanks for your reply, Micholas.
>> Are you sure about that? 'Cause I have found papers that talk about having
>> used other water models with gromos. One such is sort of a motivation for
>> the work I am doing :
>>
>> http://mb.uni-paderborn.de/fileadmin/thet/Publikationen/Veroeffentlichungen/Hydrogel-1.pdf
>>
>>
> AFAIK, no one has examined whether or not GROMOS + TIP4P is valid.  The
> water model is part of the force field, and without examining the force
> field in very well controlled simulations, I would absolutely not dive into
> simulations with water models for which the force field was not
> parametrized.
>
> A quick look at the paper suggests: "The results for OPLS-AA + SPC/E are
> in fair agreement with the experimental results" and even "Note that the
> two force field combinations that predict the correct conformations at 280
> and 360 K are not recommended by their developers. The OPLS force field was
> developed for TIP4P water and G53A6 for SPC water."
>
> Just because an application study arrived at a desirable result *does not*
> mean that the underlying physical model is valid.  You could be getting the
> "right" answer for the wrong reasons.
>
> The combination of OPLS-AA + SPC/E has been studied and found to give
> hydration free energies of amino acid analogs that are in better agreement
> than OPLS/AA + TIP*P models, and SPC/E seems to be a good choice for
> several force fields.  But this is not a choice to be made lightly, and
> just because something is published with a certain combination does not
> make it right.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613