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Merge pull request #25 from gromacstutorials/small-grammar-improvement
Small grammar improvement
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‎docs/index.html

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<span class="image">
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<img src="avatars/level1/protein-in-electrolyte/protein-in-electrolyte.png" alt="gromacs tutorial logo" />
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</span>
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<a href="sphinx/build/html/tutorials/level1/protein-in-electrolyte.html">
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<a href="sphinx/build/html/tutorials/tutorial2/protein-in-electrolyte.html">
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<div class="content">
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<p align="left">
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Simulating a <b>protein</b> in an electrolyte
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<span class="image">
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<img src="avatars/level2/stretching-a-polymer/stretching-polymer-gromacs.png" alt="gromacs tutorial logo" />
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</span>
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<a href="sphinx/build/html/tutorials/level2/stretching-a-polymer.html">
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<a href="sphinx/build/html/tutorials/tutorial3/stretching-a-polymer.html">
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<div class="content">
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<p align="left">
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Stretching a <b>polymer</b> in water

‎docs/sphinx/source/index.rst

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:caption: Tutorials
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tutorials/tutorial1/bulk-solution.rst
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tutorials/level1/protein-in-electrolyte.rst
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tutorials/level2/stretching-a-polymer.rst
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tutorials/tutorial2/protein-in-electrolyte.rst
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tutorials/tutorial3/stretching-a-polymer.rst
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tutorials/level3/solvation-energy.rst
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tutorials/level3/adsorption-ethanol.rst
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‎docs/sphinx/source/non-tutorials/links.rst

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.. |patreon| raw:: html
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<a href="https://www.patreon.com/molecularsimulations" target="_blank">patreon</a>
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<a href="https://www.patreon.com/molecularsimulations" target="_blank">patreon</a>
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.. |Protein-Data-Bank| raw:: html
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<a href="https://www.rcsb.org/structure/1CTA" target="_blank">Protein Data Bank</a>
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.. |1cta-pdb| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level1/protein-in-electrolyte/1cta.pdb" target="_blank">1cta.pdb</a>
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.. |trjconv| raw:: html
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<a href="https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html" target="_blank">trjconv</a>
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.. |empty.gro| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/empty.gro" target="_blank">empty.gro</a>
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.. |Gromos87| raw:: html
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<a href="https://manual.gromacs.org/archive/5.0.4/online/gro.html" target="_blank">Gromos87</a>
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.. |so4.gro| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/so4.gro" target="_blank">so4.gro</a>
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.. |insert-molecules| raw:: html
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<a href="https://manual.gromacs.org/2025.1/onlinehelp/gmx-insert-molecules.html" target="_blank">insert-molecules</a>
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.. |na.gro| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/na.gro" target="_blank">na.gro</a>
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.. |h2o.gro| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/h2o.gro" target="_blank">h2o.gro</a>
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.. |conf_gro_tutorial1| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/conf.gro" target="_blank">conf.gro</a>
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.. |topol-SO4.top| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/topol.top" target="_blank">topol.top</a>
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.. |forcefield.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/forcefield.itp" target="_blank">forcefield.itp</a>
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.. |h2o.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/h2o.itp" target="_blank">h2o.itp</a>
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.. |na.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/na.itp" target="_blank">na.itp</a>
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.. |so4.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/tutorial1/ff/so4.itp" target="_blank">so4.itp</a>
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.. |steepest-descent| raw:: html
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<a href="https://manual.gromacs.org/current/reference-manual/algorithms/energy-minimization.html" target="_blank">steepest-descent</a>
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.. |grace| raw:: html
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<a href="https://plasma-gate.weizmann.ac.il/Grace/" target="_blank">Grace</a>
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.. |leap-frog| raw:: html
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<a href="https://manual.gromacs.org/nightly/reference-manual/algorithms/molecular-dynamics.html#update" target="_blank">leap-frog</a>
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.. |Liese2017| raw:: html
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<a href="https://doi.org/10.1021/acsnano.6b07071" target="_blank">Liese</a>
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.. |peg-gro| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/peg.gro" target="_blank">peg.gro</a>
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.. |video_peg_youtube| raw:: html
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<a href="https://www.youtube.com/watch?v=8ldIHP175TI&t=9s" target="_blank">video</a>
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.. |download_charmm35r.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/ff/charmm35r.itp" target="_blank">charmm35r.itp</a>
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.. |download_peg.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/ff/peg.itp" target="_blank">peg.itp</a>
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.. |download_tip3p.itp| raw:: html
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<a href="https://raw.githubusercontent.com/gromacstutorials/gromacstutorials-inputs/main/level2/stretching-a-polymer/cubic-box/ff/tip3p.itp" target="_blank">tip3p.itp</a>

‎docs/sphinx/source/tutorials/level1/protein-in-electrolyte.rst

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

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.. _bulk-solution-label:
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.. include:: ../../non-tutorials/links.rst
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Ionic solution
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**************
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The first line, *Cubic box*, is a comment; the second line indicates the total
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number of atoms (0 here); and the last line defines the box dimensions in
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nanometers -- in this case, 3.5 by 3.5 by :math:`3.5~\text{nm}`. This **.gro** file
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Let us populate this empty box with :math:`\text{SO}_4^{2-}` ions first. To do so,
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This topology file for the :math:`\text{SO}_4^{2-}` ion is written in the same |Gromos87|
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==================
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‎docs/sphinx/source/tutorials/tutorial2/protein-in-electrolyte.rst

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‎docs/sphinx/source/tutorials/level2/stretching-a-polymer.rst renamed to ‎docs/sphinx/source/tutorials/tutorial3/stretching-a-polymer.rst

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