[gmx-users] how to describe the change of channel in the MD

[Justin Lemkul]

On 6/19/13 11:21 AM, aixintiankong wrote:
>
>
>   Dear,
>       In the MD, I find that when the ligand keep in the active site , the channel formed by two loops is closed. without the ligand the channel is opened. I don't know how to describe the change of channel. could i describe the channel by calculating the the most narrow distance(mass center) between the residues on the two loops? please give me some adviece. thank you very much!
>

This question was answered already:

http://lists.gromacs.org/pipermail/gmx-users/2013-June/082350.html

-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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