[gmx-users] Question regarding trjorder
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 5 22:42:29 CET 2009
Suman Chakrabarty wrote:
> 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
> [ 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
jalemkul[at]vt.edu | (540) 231-9080
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