VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jul 24 2014 - 14:59:45 CDT

Just save the frames into a DCD and load that directly into python using
https://code.google.com/p/mdanalysis/.

On 24 July 2014 20:58, Bachir Aoun <bachir.aoun_at_e-aoun.com> wrote:

> Hi
>
> I am having hard time extracting atoms coordinates from vmd to do some
> data analysis using python scripts.
> the way i am doing it right now is to export all trajectory frames in pdb
> files, read all the pdbf iles with a python script and parse the
> coordinates into a numpy array.
>
> is there any way to directly export an array of atoms coordinates along
> all trajectory configurations from vmd to a python environment (usually
> numpy).
>
> thanks
>