[gmx-users] Inconsistent shifts

Mijiddorj Batsaikhan b.mijiddorj at gmail.com
Fri Dec 16 05:30:44 CET 2016


Dear Justin,

Thank you very much.

Best regards,

Mijiddorj

>
> 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
> incompatible.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>


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