Problem in Viewing Output File in VMD

This is a discussion on Problem in Viewing Output File in VMD within the Tech Board forums, part of the Community Boards category; I am doing a Monte Carlo Simulation on Argon and viewing the output file using VMD. Here is the part ...

  1. #1
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    Problem in Viewing Output File in VMD

    I am doing a Monte Carlo Simulation on Argon and viewing the output file using VMD. Here is the part of that file:
    Code:
      21     10.000000     10.000000     10.000000      Ar    0.303895    4.327322    8.279128 Ar    9.145204    2.342695    4.070601 Ar    8.182916    0.717535    1.654591 Ar    7.572462    6.656014    5.097832 Ar    5.738435    0.753646    9.701556 Ar    0.544729    8.344379    0.667417 Ar    4.999589    0.738486    6.580141 Ar    4.890845    3.251438    7.711195 Ar    1.967732    1.611031    4.274032 Ar    9.068198    7.436556    7.508925 Ar    5.754537    6.052998    1.575422 Ar    2.424211    6.041687    9.465409 Ar    7.808051    4.058478    6.402670 Ar    1.617716    4.503045    4.084561 Ar    9.114211    0.470067    8.364241 Ar    1.318087    1.643199    1.284136 Ar    3.026772    8.354662    5.635452 Ar    4.534749    1.072564    2.679395 Ar    7.152873    9.594938    4.546791 Ar    4.228917    5.481427    5.809191 Ar    7.462603    3.352339    9.202824  21     10.000000     10.000000     10.000000      Ar     0.303895     4.327322     8.279128     Ar     9.145204     2.342695     4.070601     Ar     8.182916     0.717535     1.654591     Ar     7.572462     6.656014     5.097832     Ar     5.738435     0.753646     9.701556     Ar     0.544729     8.344379     0.667417     Ar     4.999589     0.738486     6.580141     Ar     4.890845     3.251438     7.711195     Ar     1.967732     1.611031     4.274032     Ar     9.068198     7.436556     7.508925     Ar     5.754537     6.052998     1.575422     Ar     2.424211     6.041687     9.465409     Ar     7.808051     4.058478     6.402670     Ar     1.617716     4.503045     4.084561     Ar     9.114211     0.470067     8.364241     Ar     1.318087     1.643199     1.284136     Ar     3.026772     8.354662     5.635452     Ar     4.534749     1.072564     2.679395     Ar     7.152873     9.594938     4.546791     Ar     0.000000     0.000000     0.000000     Ar     7.462603     3.352339     9.202824      21     10.000000     10.000000     10.000000      Ar     0.303895     4.327322     8.279128     Ar     9.145204     2.342695     4.070601     Ar     8.182916     0.717535     1.654591     Ar     7.572462     6.656014     5.097832     Ar     5.738435     0.753646     9.701556     Ar     0.544729     8.344379     0.667417     Ar     4.999589     0.738486     6.580141     Ar     4.890845     3.251438     7.711195     Ar     1.967732     1.611031     4.274032     Ar     9.068198     7.436556     7.508925     Ar     5.754537     6.052998     1.575422     Ar     2.424211     6.041687     9.465409     Ar     7.808051     4.058478     6.402670     Ar     1.617716     4.503045     4.084561     Ar     9.114211     0.470067     8.364241     Ar     1.318087     1.643199     1.284136     Ar     3.026772     8.354662     5.635452     Ar     4.534749     1.072564     2.679395     Ar     7.152873     9.594938     4.546791     Ar     0.000000     0.000000     0.000000     Ar     7.462603     3.352339     9.202824
    When I view the file in VMD, I got this message:
    Code:
      lenovo@ubuntu:~/Desktop$ vmd output.xyz Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012) Info) http://www.ks.uiuc.edu/Research/vmd/                          Info) Email questions and bug reports to vmd@ks.uiuc.edu            Info) Please include this reference in published work using VMD:    Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual    Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Info) ------------------------------------------------------------- Info) Multithreading available, 2 CPUs detected. Info) Free system memory: 1051MB (65%) Warning) Detected a mismatch between CUDA runtime and GPU driver Warning) Check to make sure that GPU drivers are up to date. Info) No CUDA accelerator devices available. Warning) Detected X11 'Composite' extension: if incorrect display occurs Warning) try disabling this optional X server feature. Info) OpenGL renderer: Gallium 0.4 on AMD PALM Info)   Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)  Info)   Full GLSL rendering mode is available. Info)   Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8) Info) Dynamically loaded 2 plugins in directory: Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile Info) File loading in progress, please wait. Info) Using plugin xyz for structure file output.xyz Info) Using plugin xyz for coordinates from file output.xyz Info) Determining bond structure from distance search ... xyz timestep) missing type or coordinate(s) in file 'output.xyz' for atom '1' Info) Finished with coordinate file output.xyz. Info) Analyzing structure ... Info)    Atoms: 21 Info)    Bonds: 0 Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0 Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0 Info)    Residues: 21 Info)    Waters: 0 Info)    Segments: 1 Info)    Fragments: 21   Protein: 0   Nucleic: 0 vmd >
    Thank you.
    Last edited by benner; 03-09-2012 at 06:32 PM.

  2. #2
    ATH0 quzah's Avatar
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    What does this have to do with the C programming language?


    Quzah.
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  3. #3
    and the hat of wrongness Salem's Avatar
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    Moved to tech board.
    And the OP needs to fix formatting of those stupidly long lines.
    If you dance barefoot on the broken glass of undefined behaviour, you've got to expect the occasional cut.
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