[gmx-users] vmd does not display the molecule

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 18 13:18:54 CET 2009

leila karami wrote:
> Hi
> I am trying to open a gromacs .gro file with VMD but 
> VMD gives the following message upon opening and does not display the 
> molecule : [ error reading box , unexpected  end-of-file reached ]
> I checked number of atoms specified on the second line of the gro file 
> and number of atoms really present in the file. It is ok. I also Checked 
> that the box is correctly described at the last line of my file.

Well, if everything is right then you wouldn't have an error :)  In any case, 
you haven't provided enough tangible evidence to diagnose the issue.  If you can 
post the first few and last few lines of the .gro file (i.e. "head conf.gro" and 
"tail conf.gro"), maybe someone can spot the problem.  Also, search the VMD 
mailing list, since this error has been posted there before.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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