[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.
> Mark
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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


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