[gmx-users] g_select and make_ndx
ivan.gladich at marge.uochb.cas.cz
Tue May 17 17:16:54 CEST 2011
I would like to calculate the diffusivity coefficient of water in
a slab geometry i.e. air-water-air.
One of the problem is to avoid from the calculation the waters that
evaporating from one interface to the other.
My idea was to create an index file that counts for the non-evaporating
I can do that with the tool g_select
g_select -f traj-tot.xtc -b 10000 -e 20000 -n index.ndx -s topol.tpr
-on select_index -select "all and same residue as (y> 0.2 and y< 7)"
that creates for me a new index file that, for each time step, it
conserves the index of non evaporating waters (my air-water interface is
along the y direction).
So this new index will contains 10000 (because I save the trajectory
every 1 ps) group of the name
[ all_and_same_residue_as_(y>_0.2_and_y<_7)_* ]
My question: is it possible to create a new index file that contains
only the atom index that are common to all [
all_and_same_residue_as_(y>_0.2_and_y<_7)_* ] groups?
In this way I could track all the water molecules that are not
evaporated in 10 ns simulation....
I know that make_ndx can create a new group that contains the atom
indexes that are common between all the groups..
> "group1" & "group2"....
but now I have 10000 groups....and I think I will have also problem with
the name length....
Is there a smarter way to do that?
thanks a lot for any comment or suggestions
Ivan Gladich, Ph.D.
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
e-mail: ivan.gladich at uochb.cas.cz
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