[gmx-users] g_dist

[Justin A. Lemkul]

dina dusti wrote:
> Dear Prof.
> 
> Thank you very much from your response.
> Yes, dist.xvg has four column consists origin distance and distances in 
> direction x, y , z. So distance that I want according to result of 
> g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, 
> micelle and the last carbon bounded with head group for index file.
> Also, I did this job for micelle and head group, and micelle with other 
> groups but my results (distances) were all of them near the zero.
> Please help me to obtain correct distance.
> 

Keep in mind what g_dist is measuring, center-of-mass distances.  If you select 
the micelle headgroups and then terminal carbon atoms, the positions will be 
almost coincident, as your result suggests.  Other groups that are giving a 
nearly-zero distance are likely coincident in the same 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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