[CP2K-user] [CP2K:12308] How to view .xyz file in VMD

[Travis]

Hi,

I don't have any issues either. Vasantha, I'm not familiar with the way 
you're loading the XYZ file. The output from VMD suggests you're reading it 
from a plugin, try loading the XYZ file with VMD directly (right click the 
xyz file, Open With -> VMD).

Info) Dynamically loaded 75 plugins in directory:
Info) C:/Program Files (x86)/University of 
Illinois/VMD/plugins/WIN32/molfile
Info) File loading in progress, please wait.
Info) Using plugin xyz for structure file 
C:\Users\koschey\Downloads\H2O-pos-1.xyz
Info) Using plugin xyz for coordinates from file 
C:\Users\koschey\Downloads\H2O-pos-1.xyz
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 
C:\Users\koschey\Downloads\H2O-pos-1.xyz.
Info) Analyzing structure ...
Info)    Atoms: 3
Info)    Bonds: 2
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 1
Info)    Waters: 0
Info)    Segments: 1
Info)    Fragments: 1   Protein: 0   Nucleic: 0
vmd >

-T


On Saturday, October 5, 2019 at 10:19:57 AM UTC-4, Nikhil Maroli wrote:
>
> Problem is with your VMD, the xyz file is working fine
>
> On Sat, Oct 5, 2019 at 6:35 PM vasanth kumar <va... at gmail.com> wrote:
>
>> Hi Travis
>>
>> Thank you for reply.
>>
>> When I opened .xyz file, No molecule is seen. Pl check attached file and 
>> attaching .xyz file also
>>
>>
>> On Sat, 5 Oct 2019 at 18:22, Travis <po... at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> All dumped xyz files are in standard XMOL format and so are directly 
>>> viewable in VMD. You need to load the foo-pos-1.xyz file to view the 
>>> trajectory, not your output/log file.
>>>
>>> -T
>>>
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>>
>>
>> -- 
>> With Regards
>>
>> Dr. V. Vasantha Kumar
>> Assoc. Prof. of Physics
>> Vignan Institute of Technology and Science
>> Hyderabad.
>> Mob:9959363113
>>
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>
>
> -- 
> Regards,
> Nikhil Maroli
>
>
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