dina dusti wrote:
Dear Prof.
Thank you very much from your response.
Yes, I contacted with one of them and she said me use g_dist, but I have
problem with it.
Perhaps she could be more specific. Obviously whatever you're doing with g_dist
is not working, and I honestly can't think of a way to make g_dist produce
anything I would call a "root-mean-square distance."
-Justin
Thank you again because of your patient.
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:* Thursday, February 2, 2012 2:42 PM
*Subject:* Re: [gmx-users] g_dist
dina dusti wrote:
> 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!!!
>
It's hard for anyone to speculate about an article that we haven't
read. The best course of action is to contact the corresponding author
and ask for additional information. Based on what you learn there, you
can apply similar analyses.
-Justin
> Thank you again.
> Best Regards
> Dina
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* dina dusti <dinadu...@yahoo.com <mailto:dinadu...@yahoo.com>>;
Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@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
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
========================================
--
========================================
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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