[gmx-developers] Thought on gmx distance

Justin Lemkul jalemkul at vt.edu
Wed Mar 12 14:22:38 CET 2014

Hi All,

I thought I would share a bit of feedback on the new implementation of g_dist. 
First off, I love the flexibility in the selections now, so that's great.  The 
only problem is that gmx distance does not behave like the other tools. 
Specifically, no list of available index groups is printed (default or 
otherwise, when using -n index.ndx).  I found that simply by pressing Enter when 
prompted for a selection, I can get a list of available groups, but that's not 
documented anywhere that I could find.  It was sort of a random guess when I 
stared at the screen and said, "where are my groups?"

So the suggestion I have is that gmx distance should act like the other tools 
and print a list of available groups.  That way, we don't force the user to have 
to quit the program to refer to the index file or open up a new terminal and 
then move back and forth.  I don't know if there's some technical reason why 
this isn't done already, but I thought I'd throw it out there.  Without the 
listing, I think there's an unnecessary barrier to use of the powerful selection 

If I've missed something obvious in using gmx distance, please let me know; I'm 
still getting used to the new setup of things!



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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