[gmx-users] g_select

Justin Lemkul jalemkul at vt.edu
Tue Mar 25 17:33:24 CET 2014

On 3/25/14, 12:10 PM, Josip Lovrić wrote:
> 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.

If you're using a custom group, then you need to pass an index file to g_select 
that specifies that same group.  If it's a default group, this shouldn't be an 
issue.  You can get around the above problem of incomplete residues by starting 
the selection with "same residue as" to select the whole residue that contains 
any atoms that satisfy the selection.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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