[gmx-users] Force Field Charge Parameters

[Justin A. Lemkul]

Nancy wrote:
> The OPLS-AA force field is used for glucose and trehalose in conjunction 
> with other force fields in the article by Sukit Leekumjorn and Amadeu K. 
> Sum:
> 
> "Molecular Dynamics Study on the Stabilization of Dehydrated Lipid 
> Bilayers with Glucose and Trehalose". J. Phys. Chem. B, 2008, 112 (34), 
> pp 10732–10740
> 
> Are you suggesting that the authors used incorrect parameters?
> 

Not at all.  As a matter of fact, I know them both and am familiar with their 
work.  They did a lot of work to determine that the behavior of their systems 
was consistent with reality, and that this particular force field combination 
was appropriate.

My advice to you is that you have to do your homework.  Whatever parameters you 
choose to use must be validated in light of experimental observables.  There are 
no absolute rules that any arbitrary combinations of parameters will work in 
some arbitrary system, or that any "automated" system is going to be right. 
People can get in trouble if they assume some black box is going to do correct 
work for them.

As I have said numerous times, you have to demonstrate to your audience that the 
physical model you have devised reflects reality.  This is no small task, but it 
can be done.

-Justin

> 
> On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Nancy wrote:
> 
>         Hello,
> 
>         I have successfully minimised and equilibrated two systems, one
>         consisting of a single molecule of ethylene glycol
>         (1,2-ethanediol) in a water box, and the other is one molecule
>         of glycerol, also in a water box.  I am planning to proceed to
>         simulate other sugar alcohols (e.g. erythritol, arabitol,
>         mannitol, etc).  I used topolbuild 1.2 to generate topologies
>         for ethanediol and glycerol, and for the various atoms in these
>         molecules, I used charge values from methanol (the methanol
>         tutorial included with GROMACS), i.e. +0.398 for hydroxyl
>         hydrogens, -0.574 for oxygens, and +0.176 for the carbons.
> 
> 
>     As I told you before, the origin of these charges, in the absence of
>     some published validation of the parameters, is questionable at best.
> 
> 
>         Should I use these charge values for an arbitrary sugar alcohol,
>         or should I use the charge values specified in the article:
> 
>         "OPLS All-Atom Force Field for Carbohydrates". Damm, W., A.
>         Frontera, J. Tirado-Rives, and W. L. Jorgensen. 1997. J. Comput.
>         Chem. 18:1955–1970.
> 
> 
>     If you are using OPLS, probably yes.  But as I recall, you were
>     running simulations with GROMOS96.  If this is the case, then using
>     OPLS charges or other parameters is wholly inappropriate.  The
>     simple fact is, you must use charges from the parameter set you
>     intend to simulate, otherwise go through the laborious process of
>     deriving them yourself.
> 
> 
>         Also, are there programs that will automatically generate charge
>         values and other parameters for an arbitrary molecule?
> 
> 
>     There are several options, like the R.E.D. server or antechamber
>     (available from the Amber folks), but be advised that you should
>     always follow the methodology for whatever force field you're using.
>      If it's GROMOS (like you've been using before), neither of these
>     approaches is necessary, and they may not give you correct
>     parameters.  Read the primary literature and base your decisions on
>     what you find.
> 
>     -Justin
> 
>         Thank you.
> 
>         Nancy
> 
> 
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================