.. _sphx_glr_api_gallery_md_trajectory_io:

Trajectory files
----------------

Writing molecular-dynamics trajectories to XYZ files for molecular
viewers such as VMD and OVITO, and reading them back.


.. raw:: html

  <div id='sg-tag-list' class='sphx-glr-tag-list'></div>


.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Molecular-dynamics results are usually inspected in a dedicated viewer such as VMD or OVITO, and the lowest common denominator they all read is the XYZ format: an atom count, a comment line, and one symbol x y z row per atom, repeated for every frame. write_xyz writes a whole MDResult this way. It puts the periodic box in the extended-XYZ Lattice= comment that OVITO reads, and scales the Lennard-Jones reduced lengths to angstroms (\sigma = 3.405 Å for argon), since viewers assume Å. The file is then read back with read_xyz and a frame is drawn straight from it.">

.. only:: html

  .. image:: /api/gallery/md/trajectory_io/images/thumb/sphx_glr_plot_01_vmd_xyz_trajectory_thumb.png
    :alt:

  :doc:`/api/gallery/md/trajectory_io/plot_01_vmd_xyz_trajectory`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Visualizing a trajectory: XYZ files for VMD and OVITO</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /api/gallery/md/trajectory_io/plot_01_vmd_xyz_trajectory