From: Axel Kohlmeyer (
Date: Thu Jul 24 2014 - 14:37:31 CDT

googling for "vmd numpy coordinates" returns as the first hit:


On Thu, Jul 24, 2014 at 2:58 PM, Bachir Aoun <> 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

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.