[gmx-users] Prevent protein rotation - rectangular box

[Justin Lemkul]

On 6/2/14, 7:10 AM, Steven Neumann wrote:
> Dear Users,
>
> I am trying to prevent rotation of my protein in recatngular box and I am
> thinking about applying some position restraints with the dummy atoms. I
> read some posts about this subject from 2003, 2006 but nothing recent. Is

Rather than risk wasting time by repeating things, if you're looking up 
information in old posts, please provide the links to those posts for context.

> there a gromacs tool to create a dummy atom a apply position restraints or
> maybe a pull_code would be a solution? Please, provide me with some
> information.
>

You can restrain whatever you like, and I don't necessarily see the need for a 
dummy atom in this case, but the larger question is - why do you need to prevent 
rotation?

-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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