[gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:
> Dear Prof
> 
> Thank you very much from your response.
> She said me:
> "In g_dist, when you select two groups for distance calculation, it 
> computes the distance between COM's of groups. Now, what is expected for 
> the distance between the micelle's COM and the COM of (e.g.) head 
> groups? Clearly, it's near zero ! So you should first calculate the 
> distance for each group separately and then average over all distances."
> 
> But I didn't understand what was her mean about "you should first 
> calculate the distance for each group separately and then average over 
> all distances.", because I did g_dist between micelle and for example 
> head group and then used g_analyze for dist.xvg and I had the quantity 
> near zero!!!
> 

Which is precisely what she told you.  Her suggestion is to measure the 
head-tail distance of each molecule separately, then average.  This will require 
a large number of index groups (2 groups per molecule, multiplied by however 
many molecules you have to deal with) and will be very tedious, but it can be 
done in this manner.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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