Not pytraj.load or pytraj.iterload. Both of those load full trajectory
information and give me an appropriate volume value.
pytraj.Trajectory is the one I had been using (because it was necessary for
me to get the mean structure in a prior calculation) that does not work for
pytraj.volume.
On Mon, Aug 19, 2019 at 12:29 AM Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 19 2019 - 07:00:03 PDT
