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 <[email protected]>
*To:* dina dusti <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*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> | (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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