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
Dina
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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
-- ========================================
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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