[gmx-users] g_dist

[Justin A. Lemkul]

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

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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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