[gmx-users] g_dist

[Justin A. Lemkul]

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 <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 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *To:* dina dusti <dinadusti at yahoo.com <mailto:dinadusti at yahoo.com>>; 
> Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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
>  >
>  > -- ========================================
>  >
>  > 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

========================================