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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
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