[gmx-users] crazy bonds in xtc file

Justin Lemkul jalemkul at vt.edu
Mon Nov 10 13:35:57 CET 2014

On 11/10/14 12:33 AM, RINU KHATTRI wrote:
> hello everyone
> i am working on protein ligand with popc membrane i have loaded the
> xtc file with gro file in vmd  gro is ok but xtc is showing crazy
> bonds i searched the mailing list i got trajconv command to use but
> where i am at 50ns
> i have to go back and  correct the file or i can continue where i have
> to use this trajconv
> kindly help
> http://s48.photobucket.com/user/mittukhattri/media/Screenshot_zpse0fea8a0.png.html

This is just a periodicity effect, as you have found from the previous mailing 
list posts.  There is nothing wrong with the run, and you only need to invoke 
trjconv for visualization purposes after everything is done.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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