[gmx-users] Question regarding trjorder

Suman Chakrabarty suman at sscu.iisc.ernet.in
Mon Jan 5 22:29:59 CET 2009


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?

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

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?

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

Thanks and regards,
Suman Chakrabarty.

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