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simongravelle committed Jun 28, 2024
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25 changes: 11 additions & 14 deletions docs/sphinx/source/tutorials/level1/bulk-solution.rst
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Expand Up @@ -640,8 +640,8 @@ Minimalist NVT input file

From the generated *temperature-nvt-minimal.xvg* file, one can see that temperature
started from 0 K, which was expected since the atoms have no velocity
during a minimization step, and reaches a temperature slightly larger
than the requested 360 K after a duration of a few picoseconds.
during a minimization step, and reaches a temperature slightly larger than the
requested 360 K after a duration of a few picoseconds.

.. container:: justify

Expand Down Expand Up @@ -943,25 +943,22 @@ Adjust the density using NPT

.. container:: justify

The pressure curve reveals large oscillations in the
pressure, with the pressure alternating between large negative
values and large positive values. These large oscillations are
typical in molecular dynamics, and not a source of concern here.
The pressure curve reveals large oscillations in the pressure, with the pressure alternating between large negative
values and large positive values. These large oscillations are typical in molecular dynamics, and not a source of
concern here.

Radial distribution function
============================

.. container:: justify

Let us perform a 400 pico seconds run in the
NVT ensemble, during which the atom positions will be printed every
pico-second. The trajectory will then be used to measure radial distribution
functions and probe the solvation environnement of the ions.
Let us perform a :math:`400~\text{ps}` run in the NVT ensemble, during which the atom positions will be printed every
pico-second. The trajectory will then be used to measure radial distribution functions and probe the solvation
environment of the ions.

.. container:: justify

Create a new input file within the *inputs/* folder, call it *production.mdp*,
and copy the following lines into it:
Create a new input file within the *inputs/* folder, call it *production.mdp*, and copy the following lines into it:

.. code-block:: bw
Expand Down Expand Up @@ -1014,7 +1011,7 @@ Radial distribution function
:math:`\text{SO}_4^{2-}` and
:math:`\text{H}_2\text{O}`,
as well as in between :math:`\text{H}_2\text{O}` molecules.
This can be done using the *gmx rdf* command as follow:
This can be done using the *gmx rdf* command as follows:

.. code-block:: bash
Expand All @@ -1025,7 +1022,7 @@ Radial distribution function
Selecting the sodium ions, and then the water. Repeat the same operation for
the sulfate and water, and for the water and water. For the water-water
RDF, it is better to exclude the intra-molecular contribution using
the *-excl* option, as follow:
the *-excl* option, as follows:

.. code-block:: bash
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