[gmx-users] Question regarding trjorder

[Justin A. Lemkul]

Suman Chakrabarty wrote:
> Hi,
> 
> I would like to keep only the water molecules in the first hydration
> shell for visualization purpose. Using trjorder I could successfully
> create the ordered trajectory. But I could not follow the following
> statement in the manual:
> 
> "When an index group of the first n waters is made, the ordered
> trajectory can be used ...."
> 
> How do I create this index file? Will the following entry work?

If you type "help" at the make_ndx prompt, it will give you some examples. 
There are more at:

http://wiki.gromacs.org/index.php/make_ndx

There are also some examples within the list archive on how to create specialty 
index groups.

> 
> [ Hydration Shell ]
> 1 2 3 .... n
> 

That will work to give you the hydration shell.

> Of course I'll put integers till n.
> 
> Next can I use trjconv to keep only the protein along with these n water
> molecules in the trajectory?

Yes, if you merge the Protein and Hydration Shell index groups (also using 
make_ndx).  Otherwise you can only write one or the other.

> 
> Possibly I am asking a very naive question, but I could not find a
> general guideline to write the index file in the manual.
> 

When in doubt, check the archive and the wiki :)

-Justin

> 
> Thanks and regards,
> Suman Chakrabarty.
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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