[CP2K-user] [CP2K:12311] How to view .xyz file in VMD

[vasanth kumar]

Hi Nikhil

Thank you. I loaded .xyz file and now able to see molecule.

On Sat, 5 Oct 2019 at 20:01, Travis <polla... at gmail.com> wrote:

> 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 first.
>
> 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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>


-- 
With Regards

Dr. V. Vasantha Kumar
Assoc. Prof. of Physics
Vignan Institute of Technology and Science
Hyderabad.
Mob:9959363113
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