[gmx-users] g_dist

dina dusti dinadusti at yahoo.com
Wed Feb 1 17:45:02 CET 2012

Dear Prof.

Thank you very much from your response.
but I didn't select micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but g_dist ...!!!
Where is my mistake?
I select groups in index file correctly.
Please help me.

Thank you again.
Best Regards

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, February 1, 2012 3:13 PM
Subject: Re: [gmx-users] g_dist

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 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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