[gmx-users] g_select

[Josip Lovrić]

Dear GROMACS community,

I am trying to index some molecules with g_select. I have system of
carboxylic molecules(group named MOL) forming monolayer on NaCl surface.
Some of the molecule are attached to surface and some not. With g_select I
want to select molecule which are not attached to
surface. molecules which are not attached are more far from surface so I am
using that fact.
This is line of g_select

g_select_mpi -sf select.dat -f nacl_palm_md_224.xtc -s nacl_palm_md_224.tpr
-b 4000 -e 4000 -on select.ndx

and select.dat is

not_attached = group "MOL" and not within 2 of resname Na;
not_attached;

Gromacs return me this answer selection parser: invalid selection
'not_attached = group "MOL" and not within 2 of resname Na'

When I use "resname MOL" instead of "group" it is working, but then in
index file I only have numbers of atoms ant that is useless for me.
I want to have molecules which are not attached to surface.
So obviously gromacs is not recognizing my MOL as a group, which is strange
because MOL is recognized as a energy group in my .mdp file.

Regards,
Josip