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docs/sphinx/source/tutorials/level1/bulk-solution.rst

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@@ -640,8 +640,8 @@ Minimalist NVT input file
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From the generated *temperature-nvt-minimal.xvg* file, one can see that temperature
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started from 0 K, which was expected since the atoms have no velocity
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during a minimization step, and reaches a temperature slightly larger
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than the requested 360 K after a duration of a few picoseconds.
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during a minimization step, and reaches a temperature slightly larger than the
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requested 360 K after a duration of a few picoseconds.
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.. container:: justify
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@@ -943,25 +943,22 @@ Adjust the density using NPT
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The pressure curve reveals large oscillations in the
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pressure, with the pressure alternating between large negative
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values and large positive values. These large oscillations are
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typical in molecular dynamics, and not a source of concern here.
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The pressure curve reveals large oscillations in the pressure, with the pressure alternating between large negative
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values and large positive values. These large oscillations are typical in molecular dynamics, and not a source of
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concern here.
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Radial distribution function
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============================
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.. container:: justify
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Let us perform a 400 pico seconds run in the
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NVT ensemble, during which the atom positions will be printed every
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pico-second. The trajectory will then be used to measure radial distribution
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functions and probe the solvation environnement of the ions.
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Let us perform a :math:`400~\text{ps}` run in the NVT ensemble, during which the atom positions will be printed every
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pico-second. The trajectory will then be used to measure radial distribution functions and probe the solvation
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environment of the ions.
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Create a new input file within the *inputs/* folder, call it *production.mdp*,
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and copy the following lines into it:
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Create a new input file within the *inputs/* folder, call it *production.mdp*, and copy the following lines into it:
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.. code-block:: bw
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@@ -1014,7 +1011,7 @@ Radial distribution function
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:math:`\text{SO}_4^{2-}` and
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:math:`\text{H}_2\text{O}`,
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as well as in between :math:`\text{H}_2\text{O}` molecules.
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This can be done using the *gmx rdf* command as follow:
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This can be done using the *gmx rdf* command as follows:
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.. code-block:: bash
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Selecting the sodium ions, and then the water. Repeat the same operation for
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the sulfate and water, and for the water and water. For the water-water
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RDF, it is better to exclude the intra-molecular contribution using
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the *-excl* option, as follow:
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the *-excl* option, as follows:
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.. code-block:: bash
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