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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