[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 23 19:47:12 CEST 2009
Marc Charendoff wrote:
> So sorry! You're absolutely right. Re the question on Zn 2+ I am asking
> about the ffgmx forcefield.
I don't believe the answers to your questions are in the public domain, for
several reasons. First, ffgmx is an old, deprecated force field that is
somewhat of a hodge-podge of many different parameters (reference previous
discussions on the list). For any new simulation, I would strongly recommend a
more modern force field. Second, the official reference for the Gromos87 force
field (the backbone of ffgmx) is the Gromos87 user's manual, which one has to
pay a license fee to obtain.
Based on literature of more recent Gromos96 force field parameter sets (53a5 and
53a6), I would think that coordination geometry was not involved. Other details
are still sparing regarding ion parameterization, aside from a small section
describing repulsive terms between ions in the Gromos96 53a5/53a6 paper.
> Marc Charendoff wrote:
> > Hello,
> > I am curious - is there anyway to see what assumptions were
> made when parameterizing the Zn 2+ ion? Was it tetrahedrally or
> octahedrally coordinated? With waters only or with imidazoles? Do the
> different force fields make different assumptions? Guidance appreciated.
> Without even knowing the force field to which you were referring, we
> can't say anything other than to refer you to the primary literature for
> that force field.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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