[gmx-users] trjorder and index

[Justin A. Lemkul]

Sanku M wrote:
> Hi,
>   I am trying to use trjorder command to generate a sorted trajectory 
> where all the water molecules are certain distance away. I can use the 
> trjorder command to generate the sorted trajectory where all waters are 
> sorted based on distance but I am looking for method for creating a 
> index file which will have  only those water molecules which are ,say 
> 0.4 nm away from protein. So far, I could not find any way in trjorder 
> which can give me an index file containing the water molecules certain 
> distance away. -nshell option in trjorder only gives the number of water 
> molecules within a distance but does not specify their indices.
> 
>  Also, since the water molecules are always fluctuating, the number of 
> water within a certain distance and their indexing will change all the time.
> So, I was wondering whether you can suggest a way where I can create an 
> index file from the sorted trajectory so as to have only those waters 
> which are certain distance away. I mean : is there any way in make_ndx 
> tool , where one can do it using certain keywords. 
> 

Dynamic selections can be created with g_select, not make_ndx.  The g_select 
output will be an index group for each frame, which (to my knowledge) cannot be 
automatically used by any Gromacs tool yet, but you can certainly select frames 
that correspond to these groups to write out a given frame.

The other problem is that you'll potentially have different numbers of atoms in 
each frame, making assembling a single trajectory impossible.

-Justin

-- 
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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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