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

[Eldhose Iype]

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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>
>
>