VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 24 2014 - 17:04:28 CDT

On Thu, Jul 24, 2014 at 5:33 PM, Bachir Aoun <bachir.aoun_at_e-aoun.com> wrote:
> thank you guys,
> I already know about MDanalysis, it's a package itself and uses c libraries
> to parse dcd files. Since vmd support python I was hoping there is a simple
> solution within vmd itself.

what makes you think there isn't?

>
> thanks
>
>
> On Thu, Jul 24, 2014 at 2:59 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> wrote:
>>
>> 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
>>
>>
>
>
>
> --
> Bachir AOUN 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.