fixed few typos

Author: simongravelle

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

@@ -250,10 +250,9 @@ The input files
     the small residues considered here. The *forcefield.itp* file also
     contains the list of atoms, and their respective charge in the units of
     the elementary charge :math:`e`, as well as their respective Lennard-Jones
-    parameters :math:`\sigma`
-    (in nanometer)
-    and :math:`\epsilon`
-    (in J/mol):
+    parameters :math:`\sigma` (in nanometer)
+    and :math:`\epsilon` 
+    (in kJ/mol):
 
 ..  code-block:: bw
 
@@ -268,8 +267,9 @@ The input files
 
 ..  container:: justify
 
-    Here the *ptype* is used to differential the real atoms (A) from the virtual
-    and massless site (D) from the four-point water model.
+    Here the *ptype* is used to differential the real atoms (A), such as 
+    hydrogens and oxygens, from the virtual and massless site of the
+    four-point water model (D).
 
 ..  container:: justify
 
@@ -307,7 +307,7 @@ The input files
 ..  container:: justify
 
     In this tutorial, 4 different input files will be
-    written in order to perform respectively an energy
+    written to perform respectively an energy
     minimization of the salt solution, an equilibration
     in the NVT ensemble (i.e. with fixed box size), an equilibration
     in the NPT ensemble (i.e. with changing box size), and finally

docs/sphinx/source/tutorials/level3/adsorption-ethanol.rst

@@ -80,9 +80,8 @@ Replicate the ethanol molecule
 
 ..  container:: justify
 
-    In order to create a system with several ethanol
-    molecules, let us replicate the single molecule (4x4x4
-    times) using *genconf*:
+    To create a system with several ethanol molecules, let us replicate
+    the single molecule (4x4x4 times) using *genconf*:
 
 ..  code-block:: bash
 
@@ -117,7 +116,7 @@ Create the topology file
 
 ..  container:: justify
 
-    From the same same page from the ATB repository, download the file named
+    From the same page from the ATB repository, download the file named
     |GROMACS_G54A7FF.itp| and place within *ff/*.
     Download as well the GROMACS top file named |Gromacs4.5.x-5.x.x54a7.itp|
     containing most of the force field parameters. Finally, copy
@@ -161,7 +160,7 @@ Add the water
     water configuration file |ethanol-tip4p.gro|
     and copy it in the *preparation/* folder. Then, in
     order to add (tip4p) water molecules to both gro and
-    top files, use the gmx solvate command as follow:
+    top files, use the gmx solvate command as follows:
 
 .. |ethanol-tip4p.gro| raw:: html
 
@@ -190,7 +189,7 @@ Add the water
 ..  container:: justify
 
     The created *solvated.gro* file contains the positions
-    of both ethanol and water molecules, it looks like that:
+    of both ethanol and water molecules, it looks like this:
 
 .. figure:: ../figures/level3/adsorption-ethanol/solvated-light.png
     :alt: GROMACS tutorial : Ethanol molecules in water with VMD
@@ -208,7 +207,7 @@ Add the water
 
 ..  container:: justify
 
-    In order to create a liquid-vapor slab, let
+    To create a liquid-vapor slab, let
     us increase the box size along the *x* direction to
     create a large vacuum area:
 
@@ -252,7 +251,7 @@ Energy minimization
     These 2 files have been seen in the previous
     tutorials. They contain the GROMACS commands, such
     as the type of solver to use, the temperature, etc.
-    Apply the minimisation to the solvated box using :
+    Apply the minimization to the solvated box using :
 
 ..  code-block:: bash
 
@@ -272,7 +271,7 @@ Energy minimization
 
 ..  container:: justify
 
-    During energy minimisation, the
+    During energy minimization, the
     molecules move until the forces between the atoms are
     reasonable.
 
@@ -309,7 +308,7 @@ Equilibration
 ..  container:: justify
 
     Starting from the minimized configuration, let us
-    perform a NVT equilibration for 100 ps in order to let
+    perform an NVT equilibration for 100 ps in order to let
     the system reaches equilibrium:
 
 ..  code-block:: bash
@@ -339,9 +338,9 @@ Equilibration
     :class: info
 
     The current equilibration time for the
-    NVT run (100 ps) is too small. Such short time was chosen to
+    NVT run (100 ps) is too small. Such a short time was chosen to
     make the tutorial possible to follow regardless of your computational resources.
-    Increase the duration to 1 nanosecond for a well equilibrated system.
+    Increase the duration to 1 nanosecond for a well-equilibrated system.
     Alternatively, download the final configuration I
     have obtained after a 1 ns run by clicking |ethanol-nvt_1ns.gro|.
 
@@ -364,14 +363,14 @@ Equilibration
 .. container:: figurelegend
 
     Figure: Water (blue) and ethanol (gray) density profiles along the :math:`x` axis.
-    These density profiles were obtained during the last 500 picosecond of a
+    These density profiles were obtained during the last 500 picoseconds of a
     1 nanosecond long run.
 
 ..  container:: justify
 
     The density profiles show an excess of
     ethanol at the 2 interfaces, which is commonly observed :cite:`stewart2003molecular`.
-    There is also a local maxima in the water density near center of the fluid
+    There is also a local maxima in the water density near the center of the fluid
     layer (near :math:`x = 3~\text{nm}`), and two depletion areas in between the center
     of the fluid layer and the two interfaces.
 
@@ -381,7 +380,7 @@ Imposed forcing
 ..  container:: justify
 
     To calculate the free energy profile across the liquid/vapor interface,
-    one needs to impose an additional harmonic potential to one ethanol
+    one needs to impose an additional harmonic potential on one ethanol
     molecule and force it to explore the box along the :math:`x` axis..
 
 ..  container:: justify
@@ -479,7 +478,7 @@ Imposed forcing
 ..  container:: justify
 
     You can ensure that the atom of
-    index 2 is indeed an oxygen of an ethanol molecule by
+    index 2 is indeed an oxygen atom that beyond to an ethanol molecule by
     looking at the top of the *nvt.gro* (or *nvt_1ns.gro*) file:
 
 ..  code-block:: bw
@@ -512,7 +511,7 @@ Imposed forcing
 
 ..  container:: justify
 
-    During minimisation, the ethanol molecule is separated
+    During minimization, the ethanol molecule is separated
     from the rest of the fluid until the distance between
     the center-of-mass of the 2 groups is 2 nm.
 
@@ -529,7 +528,7 @@ Imposed forcing
 ..  container:: figurelegend
 
     Figure: Ethanol molecule being pulled from the rest of the
-    fluid during minimisation and nvt equilibration.
+    fluid during minimization and NVT equilibration.
 
 ..  container:: justify
 
@@ -560,7 +559,7 @@ Imposed forcing
 
     Note that the distribution is not centered around :math:`x = 2~\text{nm}`.
     This is expected as the interactions between the pulled ethanol molecule and the
-    rest of the fluid are shifting away the average position of the 
+    rest of the fluid are shifting away from the average position of the 
     ethanol molecule from the center of harmonic potential.
 
 Free energy profile calculation
@@ -674,7 +673,7 @@ Free energy profile calculation
 
 ..  container:: justify
 
-    The durations 100 ps used in this tutorial
+    The durations of 100 ps used in this tutorial
     are too short to obtain a smooth and reliable PMF curve. Increase
     the duration of the production runs to a few
     nanoseconds for reasonable results.
@@ -689,7 +688,7 @@ Free energy profile calculation
 
 ..  container:: justify
 
-    The PMF also indicates that, once adsorbed,
+    The PMF also indicates that once adsorbed,
     the ethanol molecule requires an energy of about :math:`5~\text{kJ/mol}`
     to re-enter the liquid phase (see blue curve), which is about
     :math:`2.2~k_\text{B} T`.