VMD-L Mailing List

From: Bachir Aoun (bachir.aoun_at_e-aoun.com)
Date: Thu Jul 24 2014 - 16:33:06 CDT

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.

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