[gmx-users] Re: gmx-users Digest, Vol 89, Issue 52

[Justin A. Lemkul]

Алексей Раевский wrote:
> mm...sorry for incorrect explanation of the task. I know how to use 
> index_ndx and g_select, but I don't know whether it is possible to  
> create an index group of all atoms in !!sphere!! with a radius of 10 
> angstrom around selected "carbon" (for example). Exactly I don't know 

In this case, no, probably not.  You can get individual spheres of water around 
each carbon, which may roughly come out to what you want.

> how and where to determine a sphere's parameters. As you understand if 
> this sphere includes SOL molecules (which are flexible and all time will 
> be changing one to another from outside to the inside of the sphere), so 
> I have to define not atom numbers of SOL but constant spatial character 
> of the sphere. IS IT possible? With a use of index file it will look 
> like a new index.ndx, with [sphere] section and its content, for each frame
> 

You can only generate snapshots.  You're right, since molecules move, the 
indices are dynamic.  If you tried to get a whole trajectory with your criteria, 
almost certainly some frames would have different numbers of atoms.  Gromacs 
currently does not support this.

-Justin

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>     Hi. I've look through the manual and didn't find an answer on my
>     question:
>     i've got a trajectory and i want to convert it in *.pdb with such
>     parameters
>     of index file [all atoms within a sphere with a chosen radius around
>     selected atom]. What can i do? Thank you
> 
> 
>     --
>     *ó ��������Í!
> 
> 
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>     *
> 
>     Nemo me impune lacessit*
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>     Message: 5
>     Date: Fri, 09 Sep 2011 17:02:40 -0400
>     From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] (no subject)
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> 
> 
>     Алексей Раевский wrote:
>      > Hi. I've look through the manual and didn't find an answer on my
>      > question: i've got a trajectory and i want to convert it in *.pdb
>     with
>      > such parameters of index file [all atoms within a sphere with a
>     chosen
>      > radius around selected atom]. What can i do? Thank you
>      >
> 
>     Use g_select to generate the index group and trjconv to write the
>     file in the
>     format (and with the contents) that you want.
> 
>     -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
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 
> 
> -- 
> /С уважением!
> 
> 
> ///
> /
> 
> Nemo me impune lacessit/
> 

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

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

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