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
--
========================================
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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