[gmx-users] how can we restrain ion position?

[Justin Lemkul]

On 9/13/14 10:22 AM, Albert wrote:
> Hello:
>
> I am just wondering how can we restrain the ion positon? Shall we use genrestr
> command?
>

Is the ion diffuse in solution or bound to something else (protein, etc)? 
Position restraints are always the same, you need to apply a 
[position_restraints] directive within the appropriate [moleculetype].  genrestr 
is overkill for restraining a single ion, just write the directive by hand.  The 
main issues are: (1) if the ion is just part of the solvent, then you have to 
change ions.itp, which restrains ALL of the ions of that type and (2) if you 
want to restrain one mobile ion, you have to create a totally separate 
[moleculetype] for it.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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