diff --git a/docs/sphinx/source/tutorials/level1/bulk-solution.rst b/docs/sphinx/source/tutorials/level1/bulk-solution.rst index dd9da67..128c43e 100644 --- a/docs/sphinx/source/tutorials/level1/bulk-solution.rst +++ b/docs/sphinx/source/tutorials/level1/bulk-solution.rst @@ -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 @@ -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 @@ -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 @@ -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