@@ -640,8 +640,8 @@ Minimalist NVT input file
640640
641641 From the generated *temperature-nvt-minimal.xvg * file, one can see that temperature
642642 started from 0 K, which was expected since the atoms have no velocity
643- during a minimization step, and reaches a temperature slightly larger
644- than the requested 360 K after a duration of a few picoseconds.
643+ during a minimization step, and reaches a temperature slightly larger than the
644+ requested 360 K after a duration of a few picoseconds.
645645
646646.. container :: justify
647647
@@ -943,25 +943,22 @@ Adjust the density using NPT
943943
944944.. container :: justify
945945
946- The pressure curve reveals large oscillations in the
947- pressure, with the pressure alternating between large negative
948- values and large positive values. These large oscillations are
949- typical in molecular dynamics, and not a source of concern here.
946+ The pressure curve reveals large oscillations in the pressure, with the pressure alternating between large negative
947+ values and large positive values. These large oscillations are typical in molecular dynamics, and not a source of
948+ concern here.
950949
951950Radial distribution function
952951============================
953952
954953.. container :: justify
955954
956- Let us perform a 400 pico seconds run in the
957- NVT ensemble, during which the atom positions will be printed every
958- pico-second. The trajectory will then be used to measure radial distribution
959- functions and probe the solvation environnement of the ions.
955+ Let us perform a :math: `400 ~\text {ps}` run in the NVT ensemble, during which the atom positions will be printed every
956+ pico-second. The trajectory will then be used to measure radial distribution functions and probe the solvation
957+ environment of the ions.
960958
961959.. container :: justify
962960
963- Create a new input file within the *inputs/ * folder, call it *production.mdp *,
964- and copy the following lines into it:
961+ Create a new input file within the *inputs/ * folder, call it *production.mdp *, and copy the following lines into it:
965962
966963.. code-block :: bw
967964
@@ -1014,7 +1011,7 @@ Radial distribution function
10141011 :math: `\text {SO}_4 ^{2 -}` and
10151012 :math: `\text {H}_2 \text {O}`,
10161013 as well as in between :math: `\text {H}_2 \text {O}` molecules.
1017- This can be done using the *gmx rdf * command as follow :
1014+ This can be done using the *gmx rdf * command as follows :
10181015
10191016.. code-block :: bash
10201017
@@ -1025,7 +1022,7 @@ Radial distribution function
10251022 Selecting the sodium ions, and then the water. Repeat the same operation for
10261023 the sulfate and water, and for the water and water. For the water-water
10271024 RDF, it is better to exclude the intra-molecular contribution using
1028- the *-excl * option, as follow :
1025+ the *-excl * option, as follows :
10291026
10301027.. code-block :: bash
10311028
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