[gmx-users] index file group names: Case sensitive

Justin Lemkul jalemkul at vt.edu
Sun Mar 23 02:49:09 CET 2014

On 3/22/14, 7:41 PM, shivangi nangia wrote:
> Hello All,
> I have a question regarding case sensitivity for index file group names.
> If I have a group named "l"ipid (i.e. lipid) in the index file but I have
> it as "L"ipid (i.e. Lipid) in the .mdp file, does that matter?
> I am not getting any errors while running any gmx command but I feel my
> system is behaving funny in the sense that during umbrella sampling the
> pull group is only the protein but I the VMD images are suggesting that the
> lipid bilayer (named: LIpid/lipid) is also moving.

If grompp didn't complain, then the index group was properly read.  You can 
confirm the proper application of the index groups using gmxdump on the .tpr file.

Use of the pull code does not guarantee that any group will inherently not move, 
and perhaps whatever you are doing is simply causing the motion.  Newton's Laws 
still apply!



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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