[gmx-users] Question regarding trjorder

Suman Chakrabarty suman at sscu.iisc.ernet.in
Mon Jan 5 23:25:29 CET 2009

On Mon, 5 Jan 2009, Justin A. Lemkul wrote:

>>  [ Hydration Shell ]
>>  1 2 3 .... n
> That will work to give you the hydration shell.

Actually it seems I'll have to give the atom numbers instead of molecule 
numbers. When I used the above index group for testing, it just produced 
first n atoms of my system, i.e. part of the protein!

>>  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.

Thanks for your help. I could successfully generate the trajectory now 
using make_ndx.

I have one more question. This method works in terms of the number of 
molecules, i.e. the nearest n water molecules. But what is the way to know 
the total number of water molecules in the hydration shell? Suppose I want 
to count the number of water molecules within the first/second minimum in 
the g(r) of C-O pair. Is there a smart way to count them by specifying the 

Thanks again.


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