[gmx-users] constraining protein in the box

[Justin Lemkul]

On Tue, Dec 10, 2013 at 12:31 PM, Shine A <shine.a at iisertvm.ac.in> wrote:

> Sir,
>
>     I completed a 400 ns MD simulation. But in some part of the trajectory
> my protein is just out side the box I selected (triclinic). Is there any
> option in gromacs to constrain my protein in box during simulation.
>
>
No, nor is there any need to do so because there is no such thing as
"inside" or "outside" of an infinite system.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

-- 

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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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