[gmx-users] Groups in index.ndx

INPE (Ingrid Viveka Pettersson) inpe at novonordisk.com
Fri Jul 25 13:52:15 CEST 2014

Thank you for the help. It works fine.

BR Ingrid

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 25. juli 2014 13:36
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Groups in index.ndx

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 http://mackerell.umaryland.edu/~jalemkul

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