[gmx-users] Quick question about g_mindist

[ms]

Hi Justin,
thanks for your answer

Justin A. Lemkul ha scritto:
>> 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.

I am not looking for specific interaction now, I am only interested in
how the chain self-avoids itself in general.

However I guess from your above comment that g_mindist cannot read my
mind as I hoped :)

thanks!
m.