From what I can tell, it didn’t change the coordinates. Thank you though!
So I think i either need some options in autoimage or something akin to
cpptraj “unwrap”. For the record, I’m using a .nc trajectory file and my
simulation used an octahedral box.
Thanks!
Shayna
On Tue, Jul 2, 2019 at 4:58 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
> On Tue, Jul 2, 2019 at 4:50 PM Shayna Hilburg <shayna.hilburg.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am trying to do some analysis in python, using coordinates loaded using
> > pytraj to find the average frame with mean_structure(traj).
> > However, the protein I am analyzing has some atoms that appear far from
> the
> > molecule because of periodic boundary conditions and the simulation had
> > iwrap on. Is there a way to move the coordinates so that all bonds are
> > unbroken?
>
>
>
>
> > I believe the option is unwrap or autoimage in cpptraj? How do I
> > do 'unwrap' in pytraj?
> >
>
> Hi, may be just "traj.autoimage()"?
>
> Hai
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Received on Tue Jul 02 2019 - 15:00:02 PDT
