Hi,
Thanks for the reply.
So from the looks of it, pytraj/cpptraj ignores the 'scale_factor' variable
attribute, or at least doesn't scale the values when displaying the
trajectory object. I guess the follow up question is; in order for users to
have consistent units for all NetCDF variables in pytraj, is the only
approach to implement one's own scale_factor reader and multiplying through?
Many thanks,
Irfan Alibay
Postdoctoral Research Associate
Department of Biochemistry
The University of Oxford
On Wed, Aug 7, 2019 at 4:48 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
> Hi,
>
> I think pytraj (which is cpptraj under the hood) reads whatever velocity
> stored in the trajectory file as it is.
> It seems like parmed does the auto-conversion if traj is in amber format.
>
> In [31]: import pytraj as pt
>
>
>
> In [32]: from scipy.io import netcdf
>
>
>
> In [33]: traj = pt.iterload('trunc.nc', 'system.prmtop')
>
>
>
> In [34]: fh = netcdf.netcdf_file('./trunc.nc')
>
>
>
> In [35]: # pytraj
>
>
>
> In [36]: traj[0].velocity
>
>
> Out[36]:
> array([[-0.06234377, -0.212735 , -0.07553997],
> [-0.33413538, -0.97585237, 0.41033223],
> [ 0.28189024, 0.3869082 , 0.55642217],
> ...,
> [-0.06586777, -0.31600413, 0.39305016],
> [-0.53357279, 0.21872835, -0.2971119 ],
> [-0.28074518, -0.06457534, 0.27767515]])
>
> In [37]: # raw data (via scipy)
>
>
>
> In [38]: fh.variables['velocities'].data[0]
>
>
> Out[38]:
> array([[-0.06234377, -0.212735 , -0.07553997],
> [-0.33413538, -0.9758524 , 0.41033223],
> [ 0.28189024, 0.3869082 , 0.5564222 ],
> ...,
> [-0.06586777, -0.31600413, 0.39305016],
> [-0.5335728 , 0.21872835, -0.2971119 ],
> [-0.28074518, -0.06457534, 0.27767515]], dtype=float32)
>
> Hai
>
> On Wed, Aug 7, 2019 at 11:13 AM Irfan Alibay <irfan.alibay.lists.gmail.com
> >
> wrote:
>
> > Hi all,
> >
> > I have noticed that on reading a NetCDF restart file, parmed and pytraj
> > will report different velocity values which are off by a factor of
> 20.455.
> >
> > I unfortunately couldn't find a definite answer as to what velocity units
> > are used in parmed and pytraj respectively. So, as a sanity check, I was
> > wondering if anyone on-list could confirm that:
> >
> > parmed reports velocities in Angstroms per ps
> > pytraj reports velocities in Angstroms per 1/20.455 ps (as per
> > http://ambermd.org/formats.html)
> >
> > Many thanks,
> >
> > Irfan Alibay
> > Postdoctoral Research Associate
> > Department of Biochemistry
> > The University of Oxford
> > _______________________________________________
> > 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
>
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Received on Thu Aug 08 2019 - 12:30:02 PDT
