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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
