[gmx-users] Question regarding trjorder

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 5 23:41:35 CET 2009

Suman Chakrabarty wrote:
> 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!

Right, I was assuming that the quick example was just that, and your index group 
actually water atoms.

>>>  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 distance?

That would probably be a good time to use trjorder -nshell -r.


> Thanks again.
> Regards,
> Suman.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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