[gmx-users] Groups in index.ndx

Justin Lemkul jalemkul at vt.edu
Fri Jul 25 13:38:42 CEST 2014

On 7/25/14, 7:23 AM, INPE (Ingrid Viveka Pettersson) wrote:
> Dear Group,
> I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are disappearing. Should it be like this?

Depends on the way you're issuing make_ndx.  You can preserve the existing 
custom groups when writing a new index file by supplying the old index file as 
input to make_ndx.  If you're using default file names (hint: always provide 
your exact command!) then it will otherwise be overwritten.

make_ndx -f conf.gro -n old_index.ndx -o new_index.ndx

will preserve your custom groups and allow you to add new ones.



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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