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

[Marcin Dulak]

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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