Sanku M wrote:
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.
Dynamic selections can be created with g_select, not make_ndx. The g_select
output will be an index group for each frame, which (to my knowledge) cannot be
automatically used by any Gromacs tool yet, but you can certainly select frames
that correspond to these groups to write out a given frame.
The other problem is that you'll potentially have different numbers of atoms in
each frame, making assembling a single trajectory impossible.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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