Thanks
I was stupid as I was reading this as two different warnings but it is
connected line: "Warning Unit cell vectors are NOT rotated; imaging will
not be possible" "Warning: after the RMS-fit is performed"
So I thought imaging is not happening by default
On Sat, May 17, 2014 at 6:49 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> > On May 17, 2014, at 12:41 PM, newamber list <newamberlist.gmail.com>
> wrote:
> >
> > Hi All,
> >
> > I am running rmsd with cpptraj (14.0) but getting these warnings (even I
> > use imaged or non-imaged traj). Though as suggested imaging is not
> required
> > for rmsd option
> >
> > cpptraj input:
> >
> > trajin traj.nc #OR trajin imaged_traj.nc
> > reference initial.inpcrd
> > rms reference mass :1-324 out rms.dat
> >
> >
> > Warning: Coordinates are being rotated and box coordinates are present.
> > Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> > Warning: after the RMS-fit is performed.
> >
> >
> > I dont get these warnings when I simply image my traj as
> >
> > trajin traj.nc
> > center origin :1-324
> > image origin center familiar
> > trajout imaged_traj.nc
> >
> >
> > Thanks for any help
>
> Help with what? You didn't ask a question. The warning is
> self-explanatory. When you do a RMS fit, you rotate the system which ruins
> periodic box vector alignment. So you won't be able to image after you RMS
> fit. You can certainly image before you do that...
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Sat May 17 2014 - 11:30:02 PDT
