[gmx-users] Re: Insertion of chromium III ion into lipid bilayer
jalemkul at vt.edu
Sat Oct 19 18:42:50 CEST 2013
On 10/19/13 11:53 AM, Sathya wrote:
> Dear Justin,
> Please Tell me is there any possible option for inserting cr into into DPPC
Well, anything is possible. You'd have to define an atomtype that represents
Cr, which will involve deriving suitable LJ parameters that reproduce some
experimental observable that is in some way compatible with the underlying
theory of the lipid force field. Then you can incorporate that information into
ffnonbonded.itp and ions.itp and proceed.
As for whether or not any of that will yield a sensible simulation, I would be
highly skeptical. Additive MM force fields are not particularly adept at
dealing with highly charged ions, and transition elements are particularly
challenging because there are elements of the physics that you simply can't hope
to get right with "standard" biomolecular force fields.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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