[gmx-users] trjorder

Justin Lemkul jalemkul at vt.edu
Wed Jan 29 16:35:29 CET 2014

On 1/29/14, 9:19 AM, shahab shariati wrote:
> Hi all
> I used trjorder -f ns.xtc -s ns.tpr -n ns.ndx -o ns.pdb -nshell ns.xvg -r
> 0.74
> I encountered with Fatal error:
> An atom number in group  is larger than the number of atoms in the
> trajectory
> What means of this error? How to fix it?

It means you're telling trjorder to operate on an atom that doesn't exist. 
Either you have a problem in the way you created the index file or you didn't 
save all relevant coordinates in your .xtc file (using xtc-grps, perhaps?) but 
without more information related to both of those points, it's hard to suggest a 



Justin A. Lemkul, Ph.D.
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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