minor grammar correction

Author: simongravelle

docs/sphinx/source/tutorials/tutorial3/stretching-a-polymer.rst

@@ -187,8 +187,8 @@ And then launch the energy minimization again using:
     gmx grompp -f inputs/em.mdp -c peg-solvated.gro -p topol.top -o em
     gmx mdrun -deffnm em -v -nt 8
 
-The *define = -DFLEXIBLE* option triggers the following *if* condition
-within the *tip3p.itp* file:
+The ``define = -DFLEXIBLE`` option triggers the following **if** condition
+within the **tip3p.itp** file:
 
 ..  code-block:: bw
 
@@ -202,11 +202,11 @@ within the *tip3p.itp* file:
     ; i      j      k       funct   angle   force.c.
     2        1      3       1       104.52  628.02  104.52  628.02
     
-With this *if* condition the water molecules 
+With this **if** condition the water molecules 
 behave as flexible. This is better because rigid molecules and 
 energy minimization usually don't go along well. For the next molecular
 dynamics steps, rigid water molecules will be used by not including
-the *define = -DFLEXIBLE* command in the inputs.
+the ``define = -DFLEXIBLE`` command in the inputs.
 
 Equilibrate the PEG-water system
 ================================
@@ -215,7 +215,7 @@ Let use equilibrate the system in two steps: first a NVT simulation,
 with constant number of particles, constant volume, and imposed temperature,
 and second a NPT simulation with imposed pressure. 
 
-Within the *inputs/* folder, create a new input named *nvt-peg-h2o.mdp*,
+Within the **inputs/** folder, create a new input named **nvt-peg-h2o.mdp**,
 and copy the following lines into it:
 
 ..  code-block:: bw
@@ -255,24 +255,24 @@ Most of these commands have already been seen. In addition to the conventional
 *md* leap-frog algorithm integrator, long-range Coulomb and short-range
 van der Waals interactions, the LINCS constraint algorithm is used to maintain
 the hydrogen bonds as rigid. An initial temperature of :math:`300~K` is given
-to the system by the *gen-* commands, and the PEG is maintained in the center
-of the box by the *comm-mode* and *comm-grps* commands.
+to the system by the ``gen-`` commands, and the PEG is maintained in the center
+of the box by the ``comm-mode`` and ``comm-grps`` commands.
 
-Launch the NVT simulation using:
+Launch the *NVT* simulation using:
 
 ..  code-block:: bash
 
     gmx grompp -f inputs/nvt-peg-h2o.mdp -c em.gro -p topol.top -o nvt -maxwarn 1
     gmx mdrun -deffnm nvt -v -nt 8
 
-The *maxwarn 1* option is used to avoid a GROMACS WARNING related to the
+The ``maxwarn 1`` option is used to avoid a GROMACS WARNING related to the
 centering of the PEG in the box. 
 
-Let us follow-up with the NPT equilibration. Duplicate the *nvt-peg-h2o.mdp*
-file into a new input file named *npt-peg-h2o.mdp*. Within *npt-peg-h2o.mdp*,
-Within the *npt-peg-h2o.mdp*, delete the lines related to the creation
+Let us follow-up with the NPT equilibration. Duplicate the **nvt-peg-h2o.mdp**
+file into a new input file named **npt-peg-h2o.mdp**. Within **npt-peg-h2o.mdp**,
+Within the **npt-peg-h2o.mdp**, delete the lines related to the creation
 of velocity as its better to keep the velocities generated during the
-NVT run:
+*NVT* run:
 
 ..  code-block:: bw
 
@@ -281,7 +281,7 @@ NVT run:
     gen-seed = 65823
 
 In addition to the removal the previous 3 lines, add the following lines 
-to *npt-peg-h2o.mdp* to specify the isotropic barostat with imposed pressure
+to **npt-peg-h2o.mdp** to specify the isotropic barostat with imposed pressure
 of :math:`1~\text{bar}`:
 
 ..  code-block:: bw
@@ -292,25 +292,25 @@ of :math:`1~\text{bar}`:
     ref-p = 1.0
     compressibility = 4.5e-5
 
-Run the NPT simulation, using the final state of the NVT simulation
-*nvt.gro* as starting configuration:
+Run the *NpT* simulation, using the final state of the *NVT* simulation
+**nvt.gro** as starting configuration:
 
 ..  code-block:: bash
 
     ${gmx} grompp -f inputs/npt-peg-h2o.mdp -c nvt.gro -p topol.top -o npt -maxwarn 1
     ${gmx} mdrun -deffnm npt -v -nt 8
 
 Let us observe the evolution of the potential energy of the system during the
-3 successive equilibration steps, i.e. the *em*, *nvt*, and *npt* steps,
-using the *gmx energy* command as follow:
+3 successive equilibration steps, i.e. the energy minimization, *NVT*, and *NpT* steps,
+using the ``gmx energy`` command as follow:
 
 ..  code-block:: bash
 
     gmx energy -f em.edr -o energy-em.xvg
     gmx energy -f nvt.edr -o energy-nvt.xvg
     gmx energy -f npt.edr -o energy-npt.xvg
 
-For each of the 3 *gmx energy* commands, select *potential*.
+For each of the 3 ``gmx energy`` commands, select ``potential``.
 
 .. figure:: ../figures/level2/stretching-a-polymer/potential-energy-light.png
     :alt: Potential energy from molecular dynamics simulation in GROMACS
@@ -331,7 +331,7 @@ between the different atoms of the PEG molecules. This angle
 distribution will be used later as a benchmark to probe the effect of
 of the stretching on the PEG structure.
 
-Create a new input named *production-peg-h2o.mdp*, and copy the following
+Create a new input named **production-peg-h2o.mdp**, and copy the following
 lines into it:
 
 ..  code-block:: bw
@@ -363,8 +363,8 @@ lines into it:
     comm-mode = linear
     comm-grps = PEG
 
-This script resembles the *nvt-peg-h2o.mdp* input, but the duration and
-output frequency is different, and without the *gen-vel* commands. 
+This script resembles the **nvt-peg-h2o.mdp** input, but the duration and
+output frequency is different, and without the ``gen-vel`` commands. 
 
 Run it using:
 
@@ -373,17 +373,17 @@ Run it using:
     gmx grompp -f inputs/production-peg-h2o.mdp -c npt.gro -p topol.top -o production -maxwarn 1
     gmx mdrun -deffnm production -v -nt 8
 
-First, create an index file called *angle.ndx* using the *gmx mk_angndx*
+First, create an index file called **angle.ndx** using the ``gmx mk_angndx``
 command:
 
 ..  code-block:: bash
 
     gmx mk_angndx -s production.tpr -hyd no
 
-The *angle.ndx* file generated contains groups with all the atoms
+The **angle.ndx** file generated contains groups with all the atoms
 involved by an angle constraint, with the exception of the hydrogen
-atoms due to the use of *-hyd no*. The atom ids selected in the groups
-can be seen from the *index.ndx* file:
+atoms due to the use of ``-hyd no``. The atom ids selected in the groups
+can be seen from the **index.ndx** file:
 
 ..  code-block:: bw
 
@@ -393,8 +393,8 @@ can be seen from the *index.ndx* file:
         59    61    63    66    68    70    73    75    77    80    82    84
 
 Here, each number corresponds to the atom index, as can be seen from the 
-initial *peg.gro* file. For instance, the atom of *id 2* is a carbon atom,
-and the atom with *id 5* is an oxygen:
+initial **peg.gro** file. For instance, the atom of ``id 2`` is a carbon atom,
+and the atom with ``id 5`` is an oxygen:
 
 ..  code-block:: bw
 
@@ -410,8 +410,8 @@ and the atom with *id 5* is an oxygen:
         1PEG     H4    8   1.699   1.500   1.425  4.2893  1.6837 -0.9462
     (...)
 
-Then, extract the angle distribution from the *production.xtc*
-file using *gmx angle*:
+Then, extract the angle distribution from the **production.xtc**
+file using ``gmx angle``:
 
 ..  code-block:: bash
 
@@ -434,19 +434,18 @@ Select 1 for the O-C-C-O dihedral.
 Stretch on the polymer
 ======================
 
-Create a new folder named *elongated-box/* next to *cubic-box/*, and copy
-*ff/*, *inputs/*, *em-peg.gro*, and em-peg.tpr from *cubic-box/*
-into *elongated-box/*:
+Create a new folder named **elongated-box/** next to **cubic-box/**, and copy
+**ff/**, **inputs/**, **em-peg.gro**, and **em-peg.tpr** from **cubic-box/**
+into **elongated-box/**:
 
 To leave space for the stretched PEG molecule, let us create an
-elongated box of length :math:`6~\text{nm}`
-along the *x* direction:
+elongated box of length :math:`6~\text{nm}` along the *x* direction:
 
 ..  code-block:: bash
 
     gmx trjconv -f em-peg.gro -s em-peg.tpr -o peg-elongated.gro -center -pbc mol -box 6 2.6 2.6 
 
-Select *system* for both centering and output.
+Select ``system`` for both centering and output.
 
 Then, follow the exact same steps as previously to solvate and equilibrate
 the system:
@@ -469,9 +468,9 @@ The index file
 
 To apply a forcing to the ends of the PEG, one needs to create atom groups.
 Specificaly, we want to create two groups, each containing a single oxygen
-atom from the edges of the PEG molecules (with ID 82 and 5). In GROMACS,
+atom from the edges of the PEG molecules (with ``id 82`` and ``5``). In GROMACS,
 this can be done using and index file *.ndx*. Create a new index file
-named *index.ndx* using the *gmx make_ndx* command:
+named **index.ndx** using the ``gmx make_ndx`` command:
 
 ..  code-block:: bash
 
@@ -486,8 +485,8 @@ When prompted, type the following 4 lines to create 2 additional groups:
     name 6 End1
     name 7 End2
 
-Then, type *q* for quitting. The index file *index.ndx*
-contains 2 additional groups named *End1* and *End2*:
+Then, type ``q`` for quitting. The index file **index.ndx**
+contains 2 additional groups named **End1** and **End2**:
 
 ..  code-block:: bw
 
@@ -509,7 +508,7 @@ The input file
 
 Let us create an input file for the stretching of the PEG molecule.
 
-Create a new input file named *stretching-peg-h2o.mdp* within *inputs/*,
+Create a new input file named **stretching-peg-h2o.mdp** within **inputs/**,
 and copy the following lines in it:
 
 ..  code-block:: bw
@@ -538,9 +537,9 @@ and copy the following lines in it:
     ref_t = 300 300
     tc_grps = PEG Water
 
-So far, the script is similar to the previously created *production-peg-h2o.mdp*
-file, but without the *comm-mode* commands. To apply the constant forcing to
-the *End1* and *End2* groups, add the following lines to *production-peg-h2o.mdp*:
+So far, the script is similar to the previously created **production-peg-h2o.mdp**
+file, but without the ``comm-mode`` commands. To apply the constant forcing to
+the **End1** and **End2** groups, add the following lines to **production-peg-h2o.mdp**:
 
 ..  code-block:: bw
 
@@ -561,18 +560,18 @@ the *End1* and *End2* groups, add the following lines to *production-peg-h2o.mdp
 The force constant is requested along the *x* direction only (Y N N),
 with a force constant :math:`k = 200~\text{kJ}~\text{mol}^{-1}~\text{nm}^{-1}`. 
 
-Launch the simulation using the *-n index.ndx* option for the *gmx grompp*
+Launch the simulation using the ``-n index.ndx`` option for the ``gmx grompp``
 command to refer to the previously created index file, so that GROMACS
-finds the *End1* and *End2* groups.
+finds the ``End1`` and ``End2`` groups.
 
 ..  code-block:: bash
 
     gmx grompp -f inputs/stretching-peg-h2o.mdp -c npt.gro -p topol.top -o stretching -n index.ndx
     gmx mdrun -deffnm stretching -v -nt 8
 
-Two data files named *stretching_pullf.xvg* and *stretching_pullx.xvg*
+Two data files named **stretching_pullf.xvg** and **stretching_pullx.xvg**
 are created during the simulation, and contain respectively the
-force and distance between the 2 groups *End1* and *End2* as a function
+force and distance between the 2 groups ``End1`` and ``End2`` as a function
 of time.
 
 .. figure:: ../figures/level2/stretching-a-polymer/pull-position-light.png
@@ -601,7 +600,7 @@ by remeasuring the dihedral angle values:
     gmx mk_angndx -s stretching.tpr -hyd no -type dihedral
     gmx angle -n angle.ndx  -f stretching-centered.xtc -od dihedral-distribution.xvg -binwidth 0.25 -type dihedral -b 20 
 
-Select 1 for the O-C-C-O dihedral. Here the option *-b 20* is used to disregard
+Select 1 for the O-C-C-O dihedral. Here, the option ``-b 20`` is used to disregard
 the first 20 pico-seconds of the simulation during which the PEG has not 
 reach is final length.