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

[Justin Lemkul]

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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