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added gif for tutorial
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docs/sphinx/source/tutorials/level1/protein-in-electrolyte.rst

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@@ -7,16 +7,16 @@ Protein in electrolyte
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Simulating a solvated protein
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.. figure:: ../figures/level1/protein-in-electrolyte/protein-light.png
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:alt: Water solution of SO\ :sub:`4`\ :sup:`2-` and Na\ :sup:`+` ions visualized with VMD
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.. figure:: ../figures/level1/protein-in-electrolyte/protein-light.webp
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:alt: Protein and Na Cl ions visualized with VMD
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:class: only-light
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:height: 250
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:height: 300
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:align: right
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.. figure:: ../figures/level1/protein-in-electrolyte/protein-dark.png
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:alt: Water solution of SO\ :sub:`4`\ :sup:`2-` and Na\ :sup:`+` ions visualized with VMD
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.. figure:: ../figures/level1/protein-in-electrolyte/protein-dark.webp
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:alt: Protein and Na Cl ions visualized with VMD
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:class: only-dark
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:height: 250
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:height: 300
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:align: right
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.. container:: justify
@@ -224,14 +224,6 @@ Run an energy minimization
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energy decreases from :math:`-3 \mathrm{e}-4~\text{kJ}/\text{mol}` to
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:math:`-1.8 \mathrm{e}-5~\text{kJ}/\text{mol}`.
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.. container:: justify
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The system can be visualized using VMD:
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.. code-block:: bash
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vmd min.gro min.trr
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Add the salt
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============
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gmx energy -f min-s.edr -o potential-energy-minimization-s.xvg
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.. container:: justify
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The system can also be visualized using VMD using:
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.. code-block:: bash
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vmd min.gro min.trr
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.. figure:: ../figures/level1/protein-in-electrolyte/protein-solvated.png
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:alt: Gromacs tutorial protein in water and salt
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.. container:: figurelegend
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Protein solvated in water. On the left, only the water molecules that are
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near the protein are represented. On the right, the entire system is shown.
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Water molecules are represented as red and white sticks, and ions are
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represented as spheres.
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Run the molecular dynamics
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==========================
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