[gmx-users] Question regarding trjorder

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 5 22:42:29 CET 2009

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:


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 :)


> 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


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