[gmx-users] Question regarding trjorder

[Justin A. Lemkul]

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.

-Justin

> Thanks again.
> 
> 
> Regards,
> Suman.
> 
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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