[gmx-users] center of mass and box co-ordinates

[Justin Lemkul]

On 5/7/13 1:05 AM, Arunima Shilpi wrote:
> Hello Justin sir
>
> In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
> the criteria used to determine the coordinates of center of mass and box
> size which you have takes as
>
> editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
> 6.560 4.362 12
>

The protein complex is centered in x and y, and the z-dimension provides 
sufficient space to allow for pulling of 5 nm.

-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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