[gmx-users] Force Field Charge Parameters
nancy5villa at gmail.com
Mon Aug 10 23:54:03 CEST 2009
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
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.
Also, are there programs that will automatically generate charge values and
other parameters for an arbitrary molecule?
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