[gmx-users] Defining a limited space for the movement of Ion

[Justin Lemkul]

On 8/8/16 7:10 AM, Alexander Alexander wrote:
> Dear Gromacs user,
>
> I have defined a "molecule = A" and a single ion together as
> "[moleculetype] = A + Ion" in my simulations. But, I get some problem when
> Ion goes so far away from the molecule A, because physically I would have a
> separated molecules defined as [moleculetype], so, I want somehow keep the
> Ion close to the molecule in simulation, I mean just in physically
> meaningful-limited sphere around the the molecule.
> Would you please let me know how I can do that?
>

Use either the pull code or a spherical flat-bottom restraint on the ion.

-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 629
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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