[gmx-users] Quick question about g_mindist

[Justin A. Lemkul]

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.

-Justin

> thanks!
> 
> m.
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

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

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

========================================