hi Shayna,
How did you get the pytraj.Trajectory. The code below using pytraj.load
seems fine to me
In [11]: import pytraj as pt
In [12]: traj = pt.load('tz2.ortho.nc', 'tz2.ortho.parm7')
In [13]: pt.volume(traj)
Out[13]:
array([53370.07989848, 53340.75205896, 53332.52759063, 53356.15921761,
53276.40269261, 53277.02435214, 53338.94154946, 53307.68715816,
53365.90922305, 53418.85444185])
Hai
On Sun, Aug 18, 2019 at 9:04 PM Shayna Hilburg <shayna.hilburg.gmail.com>
wrote:
> I figured out the issue, but thank you for the help!
> Turns out I was using pt.Trajectory to load the files but should have been
> using pt.iterload. I'm not certain why this changes the output, but the
> pt.volume function definitely only works with iterload and gives an array
> of -1 values if I use Trajectory.
>
> Thanks!
> -Shayna
>
>
> On Fri, Aug 16, 2019 at 6:30 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > Hi,
> >
> > Can you please post exact commands for cpptraj and pytraj you’ve tried?
> >
> > Hai
> >
> > On Fri, Aug 16, 2019 at 5:56 PM Shayna Hilburg <shayna.hilburg.gmail.com
> >
> > wrote:
> >
> > > Hi all,
> > >
> > > I am looking to find the volume of an NPT simulation done in a
> truncated
> > > octahedron simulation box.
> > > In CPPTRAJ, the volume command works. However, in pytraj, I just get an
> > > array of -1 values regardless of mask. Is there a way to calculate the
> > > simulation cell volume in pytraj?
> > > I'd like to use this to better understand and compare my number density
> > > data.
> > >
> > > Thank you!
> > > Best,
> > > Shayna Hilburg
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Received on Sun Aug 18 2019 - 21:30:02 PDT
