[gmx-users] g_dist

[dina dusti]

Dear Prof

Thank you very much from your response.
She said me:

"In g_dist, when you select two groups for distance calculation, it 
computes the distance between COM's of groups. Now, what is expected for the distance between the micelle's COM and the COM of (e.g.) head 
groups? Clearly, it's near zero ! So you should first calculate the 
distance for each group separately and then average over all distances."

But I didn't understand what was her mean about "you should first calculate the 
distance for each group separately and then average over all distances.", because I did g_dist between micelle and for example head group and then used g_analyze for dist.xvg and I had the quantity near zero!!!

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 6:07 PM
Subject: Re: [gmx-users] g_dist
 


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

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