[gmx-users] Re: Insertion of chromium III ion into lipid bilayer

[Justin Lemkul]

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
> bilayer.
>

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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