Just curious: can you make it work in cpptraj?
Cc Dan
Hai
On Tue, Jul 2, 2019 at 5:32 PM Shayna Hilburg <shayna.hilburg.gmail.com>
wrote:
> 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 - 15:30:02 PDT
