[gmx-users] Quick question about g_mindist

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 1 21:54:47 CET 2009

ms wrote:
> Hi,
> I am using g_mindist to see how close get C-alphas to each other in my
> chains. What I do is selecting C-alpha two times when prompted. I have
> only a quick question, just to be sure: The script doesn't take into
> account the distance between *neighbouring C-alpha*, isn't it?

I don't see why they wouldn't be.  I suppose you'd have to look into the code to 
be sure.  But if you choose C-alpha for analysis, then I would imagine all of 
those atoms are going to be considered.

If there are specific interactions you are looking for, create specific index 
groups for those residues, otherwise I don't know if you're going to gain much 
from this analysis, because the minimum distance within a protein may always 
occur between two specific atoms, oscillating about a certain value.


> thanks!
> m.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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