[gmx-users] Inconsistent shifts

Justin Lemkul jalemkul at vt.edu
Thu Dec 15 15:50:13 CET 2016

On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote:
> Dear Justin,
> Thank you very much for reply.
> My commands
> gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump
> gmx trjconv -s ../step7_1.tpr -f md_nojump.xtc -pbc mol  -ur compact -n
> ../index.ndx -fit transxy -o md_noPBC.xtc
> I got the inconsistent shifts error middle of the trajectory.

Don't use -pbc and -fit simultaneously.  Do -pbc mol then do whatever fitting 
you want.  Simultaneously trying to re-wrap PBC and apply any sort of fitting is 



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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