It's possible there are just density issues as Dave suggested. If you
would like, send me off-list the topology file and 1 or 2 frames which
illustrate the issue you are seeing so I can try to reproduce it.
-Dan
On Thu, Sep 22, 2022 at 3:42 AM <gsormani.ictp.it> wrote:
>
> Hello,
> I am using cpptraj version V5.1.0 (the simulation is in Amber2020). It
> should not be so old. Also, I just take the traj as it is and perform
> autoimage, so I think there shouldn't be rotations..
>
> Giulia
>
> > Hi,
> >
> > What version of cpptraj are you using? This sounds like it might be an
> > older one that doesn’t handle imaging after a unit cell rotation ( from
> > e.g. rms fit).
> >
> > -Dan
> >
> > On Wed, Sep 21, 2022 at 12:04 PM Giulia Sormani via AMBER
> > <amber.ambermd.org>
> > wrote:
> >
> >> Good evening to all,
> >> I am running a NVT simulation of Zr(4+) ion and 4 CL(-1, added to
> >> neutralize the charge) in a cuboid box of water.
> >> I then use the "autoimage" command of cpptraj to visualize the traj
> >> correctly.
> >> By default, the Zr (first atom of the topology) is blocked in the center
> >> of the box and all the other atoms should be imaged freely.
> >> However, the water box doesn't maintain the cuboid shape, it is
> >> deformed,
> >> for examples some voids are created at the edges of the box.
> >> What should I do to visualize the traj correctly?
> >> I did some trials changing the "fixed" and "mobile" masks, but with no
> >> success.
> >>
> >> Hope someone can help,
> >>
> >> Giulia
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
>
>
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Received on Thu Sep 22 2022 - 07:00:03 PDT
