[gmx-users] Fwd: Implicit solvent simulation

Justin Lemkul jalemkul at vt.edu
Mon Feb 10 16:06:29 CET 2014

On 2/10/14, 7:47 AM, prasun kumar wrote:
> Dear All
> I am planning to study the effect of adding the ions on the dodecamer
> protein.
> For this purpose I need to add ions (Fe2+) in the system. Any suggestion
> for it. I have come to know through  various discussion forums that  there
> is no need of adding ions to make the system neutral, but in my case I have
> to add ions, how will be mdp file look for ions added system.

You wouldn't use genion in this case.  In the case of implicit solvent, there's 
nothing to delete to replace with the ions.  genbox -ci -nmol is what you want 
here, though it is questionable whether this sort of representation is at all 
meaningful.  Hydrated ions (especially transition metals) have very complex 
properties.  I'd suspect in an implicit solvent system, a lot of the behavior 
will not represent reality.



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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