@@ -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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-
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Add the salt
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============
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@@ -284,6 +276,24 @@ Add the salt
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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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+
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Run the molecular dynamics
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==========================
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