[gpaw-users] How to convert .traj to xyz/pdb format

[Eldhose Iype]

Thank you Marcin for the help.

Cheers
Eldhose


On Tue, Jul 17, 2012 at 1:06 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk> wrote:
> On 07/17/12 12:45, Lars Smykalla wrote:
>> Did you try the ASE gui? It can visualise the structures in the traj-file
>> and save to another format if this is what you aim for.
> yes, once you have a traj file with many steps, open it with ag and save
> as xyz/pdb (will contain all the steps).
>
> Marcin
>>
>>
>>
>> Am 17.07.2012, 12:33 Uhr, schrieb Eldhose Iype<nickytenner at gmail.com>:
>>
>>> Yes, in xyz or pdb format it should be possible to write more than one
>>> configurations (structures for more than one time step) in a single
>>> file.
>>> Then they can be easily visualized using jmol, rasmol, VMD etc.
>>>
>>> What I want is just to append instead of overwrite the configurations
>>> at every time step using the write command in ASE.
>>>
>>> The problem with traj file is that it is binary and I need the
>>> coordinates in ascii format.
>>>
>>> Regards
>>> Eldhose
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Jul 17, 2012 at 12:26 PM, Jess Wellendorff<jesswe at fysik.dtu.dk>
>>> wrote:
>>>> Is the xyz format intended to be able to contain more than one
>>>> structure at
>>>> the same time?
>>>> Traj-files easily do this, but I'm not sure about xyz-files...
>>>>
>>>> - J
>>>>
>>>>
>>>> On 07/17/2012 12:12 PM, Eldhose Iype wrote:
>>>>> Dear Jess,
>>>>>
>>>>> Thank you for  your reply.
>>>>>
>>>>> Well, What I need is to write the trajectory during an MD run.
>>>>> If I use "write ('filename.xyz',mysystem)", then it overwrites the
>>>>> coordinates at every step.
>>>>>
>>>>> I want to append the coordinates to the file instead of overwrite.
>>>>>
>>>>> Regards
>>>>> Eldhose
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jul 17, 2012 at 12:07 PM, Jess Wellendorff
>>>>> <jesswe at fysik.dtu.dk>
>>>>> wrote:
>>>>>> Hi Eldhose,
>>>>>>
>>>>>> the ase.io.read and ase.io.write methods are used for this:
>>>>>>
>>>>>> https://wiki.fysik.dtu.dk/ase/ase/io.html#module-io
>>>>>>
>>>>>> - Jess W.
>>>>>>
>>>>>> On 07/17/2012 12:00 PM, Eldhose Iype wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> Could some one tell me if it is possible to convert my .traj
>>>>>>> trajectory file to either xyz or pdb format?
>>>>>>>
>>>>>>> Regards
>>>>>>> Eldhose
>>>>>>> _______________________________________________
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>>>>>>
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