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

[Lars Smykalla]

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.



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
>>>>> _______________________________________________
>>>>> gpaw-users mailing list
>>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>
>>>>
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>>
>>
>>
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