[gmx-users] Re: trjconv centre protein

[Justin Lemkul]

On 3/19/13 8:00 AM, Ewaru wrote:
> HI Justin,
>
> Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the
> protein has to be in the center (inside the box) before the simulation, is
> it?
>

Absolutely not.  In a periodic system, there is no such thing as a center. 
Centering within the central unit cell is merely a visualization convenience. 
The MD algorithm could care less.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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