[gmx-users] g_dist

dina dusti dinadusti at yahoo.com
Thu Feb 2 11:53:21 CET 2012

Dear Prof.

Thank you very much from your response.
OK, I use from g_gyrate for all of radius, but I still don't understand that what thing did they use in their articles for root-mean-square distance because they compared this quantity with quantity of obtained from gyration!!!

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: Thursday, February 2, 2012 12:08 AM
Subject: Re: [gmx-users] g_dist

dina dusti wrote:
> Dear Prof.
> Thank you very much from your response.
> He answer me that I should use from g_gyration for radius of micelle, but what should I do for hydrocarbon (dry) core or calculation of inner core of micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)?

Use g_gyrate, with a custom index group that contains the atoms of interest.  If you're interested in the radius of the hydrocarbon atoms, make that an index group and perform the analysis on it.


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

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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