[gmx-users] g_dist

dina dusti dinadusti at yahoo.com
Wed Feb 1 20:28:41 CET 2012

Dear Prof.

Thank you very much for your help.
Yes, I also used from g_rdf and g_gyrate but I am seeking "root-mean-square distance" that there is in many articles for calculation of radius of micelle and radius of dry core (hydrocarbone). I understood that they used g_dist but it doesn't work me. Perhaps I am wrong about required program (command) for calculation of root-mean-square distance?
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 9:15 PM
Subject: Re: [gmx-users] g_dist

dina dusti wrote:
> 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 ...!!!

g_dist and g_gyrate work in different ways.  You can't equate their output.

A micelle is (roughly) a sphere.  The COM of the headgroups will be the center of the sphere.  Thus, the COM of the micelle is the COM of the sphere and the COM of the headgroups is (approximately) coincident.  Hence why you are getting a very tiny distance reported by g_dist.

> Where is my mistake?
> I select groups in index file correctly.
> Please help me.

g_rdf might be a better option, by selecting the COM of the micelle as the reference and the headgroups as the group for calculation.  That way you will get the distribution of headgroup distances from the COM of the micelle, thus approximately the radius of the micelle.


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

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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