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docs/sphinx/source/tutorials/tutorial1/bulk-solution.rst

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@@ -534,31 +534,31 @@ GROMACS. In the terminal, type:
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.. code-block:: bash
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gmx energy -f min.edr -o min-pe.xvg
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gmx energy -f min.edr -o min-Ep.xvg
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Choose ``potential`` by typing ``5`` (the number may differ in your case),
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then press ``Enter`` twice.
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Here, the portable energy file **min.edr** produced
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by GROMACS during the minimization run is used, and the
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result is saved a **.xvg** file named **min-pe.xvg**. **.xvg** files
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result is saved a **.xvg** file named **min-Ep.xvg**. **.xvg** files
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can be oppened with the Grace software (or equivalent) :cite:`grace`:
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.. code-block:: bash
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xmgrace min-pe.xvg
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.. figure:: figures/potential-energy-min-light.png
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.. figure:: figures/min-Ep.png
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:alt: Gromacs tutorial : plot of the energy versus time.
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:class: only-light
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.. figure:: figures/potential-energy-min-dark.png
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.. figure:: figures/min-Ep-dm.png
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:alt: Gromacs tutorial : plot of the energy versus time.
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:class: only-dark
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.. container:: figurelegend
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Figure: Evolution of the potential energy :math:`E_\text{p}` as a function of the
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Figure: Evolution of the potential energy, :math:`E_\text{p}`, as a function of the
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number of steps during energy minimization.
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One can see from the energy plot that the potential energy is initially quite large,
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docs/sphinx/source/tutorials/tutorial1/figures/min-Ep.ipynb

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