How to view .xyz file in VMD

vasanth kumar

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Oct 5, 2019, 2:34:48 AM10/5/19

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Hi
I am trying to view .xyz file via VMD, but it is displaying line to line error by displaying total data which is in inout file.
How to set VMD to CP2K?

Thank you

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vasanth kumar

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Oct 5, 2019, 9:05:35 AM10/5/19

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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 <polla...@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

screenshot.png

H2O-pos-1.xyz

Nikhil Maroli

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Oct 5, 2019, 10:19:57 AM10/5/19

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Problem is with your VMD, the xyz file is working fine

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Regards,

Nikhil Maroli

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vasanth kumar

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Oct 5, 2019, 10:54:22 AM10/5/19

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Hi Nikhil

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

On Sat, 5 Oct 2019 at 20:01, Travis <polla...@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 <vasan...@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 <polla...@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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