[gmx-users] trjorder and index

[Sanku M]

Hi,
  I am trying to use trjorder command to generate a sorted trajectory where all 
the water molecules are certain distance away. I can use the trjorder command to 
generate the sorted trajectory where all waters are sorted based on distance but 
I am looking for method for creating a index file which will have  only those 
water molecules which are ,say 0.4 nm away from protein. So far, I could not 
find any way in trjorder which can give me an index file containing the water 
molecules certain distance away. -nshell option in trjorder only gives the 
number of water molecules within a distance but does not specify their indices.

 Also, since the water molecules are always fluctuating, the number of water 
within a certain distance and their indexing will change all the time.
So, I was wondering whether you can suggest a way where I can create an index 
file from the sorted trajectory so as to have only those waters which are 
certain distance away. I mean : is there any way in make_ndx tool , where one 
can do it using certain keywords. 

Any help will be really appreciated.
Sanku
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