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update tutorial
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simongravelle committed May 28, 2024
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Expand Up @@ -387,10 +387,11 @@ Run the molecular dynamics

As the simulation progresses, the volume of the box decreases and better
adjust to the fluid content of the box, as can be seen using *gmx energy*
and choosing *volume*:
and extracting the *volume*, and/or by extracting the *density*:

.. code-block:: bash
gmx energy -f npt.edr -o potential-energy-npt.xvg
gmx energy -f npt.edr -o volume-npt.xvg
gmx energy -f npt.edr -o density-npt.xvg
.. include:: ../../non-tutorials/accessfile.rst

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