[gmx-users] Distance restraint between two chains' com

[Justin Lemkul]

On 2/5/15 2:39 AM, WT Ren wrote:
> Dear Gromacs Users,
>
> I am trying to apply a distance restraint between two chains' center of
> mass to  prevent them diffusing far away from each other. As I known, the
> pull code seems only can restrain the distance to a reference distance with
>   harmonic potential, while the distance restraint seems can not be applied
> to center of mass.
>
> So can anyone help on this issue?
>

I am assuming that you want to apply some sort of flat-bottom potential, to be 
applied only when the chains move a certain distance.  Indeed the pull code 
cannot do that at present, but a flat-bottom potential is in development if you 
want to test it:

https://gerrit.gromacs.org/#/c/3947/

-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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