[gmx-users] Force Field: A new chemical compound

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 3 21:00:24 CEST 2008

Chih-Ying Lin wrote:
> Hi
> Honestly, I don't know how to do the quantum chemistry calculation.
> I have the one azobenzene derivative force field parameters(from QM/MM
> paper) in hand.
> This azobenzene derivative is quite similar with the azotab compound,
> which I need.
> For the rest parts of the azotab compound I try to used the default
> force field parameters, which come from either Amber or Gromacs
> package.
> Will it be reasonable to determine the force field parameters of the
> new compound like I mentioned above?
> Azotab will put into water; however, the force field parameters of the
> azobenzene derivative are coming from the QM/MM calculation in gas
> phase. So, will it be wrong afterall?

The general answer to this type of question is that you have to derive 
the parameters for a compound in a way that is compatible with the force 
field you choose to use.  For an AMBER-type force field, quantum 
calculations may be in order.  For a FF like OPLS and GROMOS, empirical 
derivation/adjustment and free energy calculations are the correct protocol.

Bottom line: read that paper regarding the derivation of the force field 
you want, and follow that methodology.


> Thanks a lot
> Lin
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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