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small grammar improvement
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‎docs/sphinx/source/non-tutorials/links.rst

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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/tutorial3/stretching-a-polymer.rst

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@@ -21,42 +21,30 @@ Stretching a polymer
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:class: only-light
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The goal of this tutorial is to use GROMACS and solvate a small
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hydrophilic polymer in a reservoir of water.
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hydrophilic polymer in a reservoir of water.
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An all-atom description is used for both polymer and water. The polymer is
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PolyEthylene Glycol (PEG). Once the system is properly
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equilibrated at the desired temperature and pressure, a force is applied
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to both ends of the polymer. The evolution of the polymer length
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is measured, and the energetics of the system is measured.
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PolyEthylene Glycol (PEG). Once the system is properly equilibrated at the
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desired temperature and pressure, a force is applied to both ends of the
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polymer. The evolution of the polymer length is measured, and the energetics
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of the system is analyzed. This tutorial was inspired by a publication by
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|Liese2017| and coworkers, in which molecular dynamics simulations are
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compared with force spectroscopy experiments :cite:`lieseHydrationEffectsTurn2017`.
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..
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(GROMOS 54A7 force
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field :cite:`schmid2011definition`)
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(SPC flexible model :cite:`wu2006flexible`)
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This tutorial was inspired by a |Liese2017| by Liese and coworkers, in which
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molecular dynamics simulations are
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compared with force spectroscopy experiments :cite:`liese2017hydration`.
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.. |Liese2017| raw:: html
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<a href="https://doi.org/10.1021/acsnano.6b07071" target="_blank">publication</a>
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.. include:: ../../non-tutorials/recommand-salt.rst
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.. include:: ../../non-tutorials/needhelp.rst
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.. include:: ../../non-tutorials/GROMACS2024.2.rst
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Prepare the PEG molecule
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========================
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Download the *peg.gro* file for the PEG molecule by clicking |download_H2O.data|.
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The *peg.gro* file can be visualized using vmd, by typing in a terminal:
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.. |download_H2O.data| 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">here</a>
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Download the |peg-gro| file for the PEG molecule by clicking. The
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**peg.gro** file can be visualized using VMD, by typing in a terminal:
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.. code-block:: bash
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oxygen atoms (in red), and hydrogen atoms (in white). See
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the corresponding |video_peg_youtube|.
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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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Save **peg.gro** in a new folder. Next to **peg.gro** create an empty
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file named **topol.top**, and copy the following lines into it:
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Save *peg.gro* in a new folder. Next to *peg.gro* create an empty
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file named *topol.top*, and copy the following lines in it:
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.. code-block:: bw
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.. code-block:: bash
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[ defaults ]
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; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
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1 1 no 1.0 1.0
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; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
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1 1 no 1.0 1.0
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; Include forcefield parameters
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#include "ff/charmm35r.itp"
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#include "ff/peg.itp"
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#include "ff/tip3p.itp
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#include "ff/tip3p.itp"
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[ system ]
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; Name
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PEG
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PEG
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[ molecules ]
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; Compound #mols
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PEG 1
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Next to *conf.gro* and *topol.top*, create a folder named *ff/*, and copy
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the following 3 *.itp* files into it: |download_charmm35r.itp|, |download_peg.itp|,
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and |download_tip3p.itp|.
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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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PEG 1
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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>
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These 3 files contain the parameters for the PEG and the water molecules
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Next to **conf.gro** and **topol.top**, create a folder named **ff/**, and copy
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the following 3 **.itp** files into it: |download_charmm35r.itp|, |download_peg.itp|,
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and |download_tip3p.itp|. These 3 files contain the parameters for the PEG and the water molecules
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with oxygen (OW) and hydrogen (HW) atoms.
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Create an *inputs/* folder next to *ff/*, and create a new empty file
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called *em.mdp*. Copy the following lines into it:
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Create an **inputs/** folder next to **ff/**, and create a new empty file
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called **em.mdp**. Copy the following lines into it:
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.. code-block:: bw
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rvdw = 1
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pbc = xyz
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Most of these commands have been seen in previous tutorials. The most
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important command is *integrator = steep*, which set the algorithm
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used by GROMACS as the steepest-descent,
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which moves the atoms following the direction of the largest forces
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until one of the stopping criteria is reached :cite:`debyeNaeherungsformelnFuerZylinderfunktionen1909`.
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Most of these commands have been seen in previous tutorials. Arguably the
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most important command is ``integrator = steep``, which sets the algorithm
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used by GROMACS as the steepest-descent method. This algorithm moves the
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atoms following the direction of the largest forces until one of the stopping
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criteria is reached :cite:`debyeNaeherungsformelnFuerZylinderfunktionen1909`.
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Run the energy minimization using GROMACS by typing in a terminal:
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gmx grompp -f inputs/em.mdp -c peg.gro -p topol.top -o em-peg
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gmx mdrun -deffnm em-peg -v -nt 8
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The *-nt 8* option limits the number of threads that GROMACS uses. Adjust
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the number to your computer.
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The ``-nt 8`` option limits the number of threads that GROMACS uses. Adjust
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the number to your computer.
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After the simulation is over, open the trajectory file with VMD by typing
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in a terminal:
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vmd peg.gro em-peg.trr
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From VMD, the PEG molecule can be seen moving a little by the
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steepest-descent algorithm.
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steepest-descent algorithm.
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Before adding the water, let us reshape the box and recenter the PEG molecule
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in the box. As a first step, let us use a cubic box of
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lateral size :math:`2.6~\text{nm}`.
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Before adding the water, let us reshape the box and recenter the PEG
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molecule in the box. As a first step, let us use a cubic box of lateral
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size :math:`2.6~\text{nm}`.
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.. code-block:: bash
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.. code-block:: bash
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gmx trjconv -f em-peg.gro -s em-peg.tpr -o peg-recentered.gro -center -pbc mol -box 2.6 2.6 2.6
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gmx trjconv -f em-peg.gro -s em-peg.tpr -o peg-recentered.gro -center
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-pbc mol -box 2.6 2.6 2.6
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Select *system* for both centering and output. The newly created *gro*
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file named *peg-recentered.gro* will be used as a starting point
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for the next step of the tutorial.
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Select ``system`` for both centering and output. The newly created **.gro**
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file named **peg-recentered.gro** will be used as a starting point for the
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next step of the tutorial.
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Solvate the PEG molecule
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========================

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