[gmx-users] g_select

Justin Lemkul jalemkul at vt.edu
Wed Mar 26 16:38:28 CET 2014

On 3/26/14, 11:30 AM, Josip Lovrić wrote:
> Hello,
> I managed to create notattached group but now it is not recognizing system
> group when I compile it with gromp.
> I get this answer:
> Fatal error:
> Group system referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
> This is my grompp line:
> grompp_mpi -f md.mdp -c nacl_palm_md_224.gro -p topol_nc.top -o
> nacl_palm_md_224_na.tpr -n select.ndx
> group system is defined like this in .top file:
> [ system ]
> ; Name
> NaCl
> P.S.
> Feel free to ask me more information, I am quite new in gromacs and I am
> not sure if I am giving you all the information.

The [system] directive just gives a name for output coordinate files and such. 
It is not equivalent to the "System" index group.

When reporting errors with groups, index files, etc, you need to provide the 
text of the .mdp file and, at minimum, a listing of the groups in the index 
file, e.g. from gmxcheck.



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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