Fixed some typos in new documentation

src/adjmat/HbondMatrix.cpp

@@ -45,7 +45,7 @@ a_{ij} = \sigma_{oo}( \mathbf{r}_{ij} ) \sum_{k=1}^N \sigma_{oh}( \mathbf{r}_{ik
 This expression was derived by thinking about how to detect if there is a hydrogen bond between atoms $i$ and $j$.  The notion is that
 if the hydrogen bond is present atoms $i$ and $j$ should be within a certain cutoff distance.  In addition, there should be a hydrogen
 within a certain cutoff distance of atom $i$ and this hydrogen should lie on or close to the vector connecting atoms $i$ and $j$.
-As such $\sigma_{oo}( \mathbf{r}_{ij} )$ is a switching function that acts on the modulus of the vector connecting atom $i$ to atom
+As such $\sigma_{oo}(\mathbf{r}_{ij})$ is a switching function that acts on the modulus of the vector connecting atom $i$ to atom
 $j$.  The sum over $k$ then runs over all the hydrogen atoms that are specified using using HYDROGEN keyword.  $\sigma_{oh}(\mathbf{r}_{ik})$
 is a switching function that acts on the modulus of the vector connecting atom $i$ to atom $k$ and $\sigma_{\theta}(\theta_{kij})$
 is a switching function that acts on the angle between the vector connecting atoms $i$ and $j$ and the vector connecting atoms $i$ and

src/adjmat/Neighbors.cpp

@@ -31,14 +31,14 @@ nearest atoms to each of the first 100 atoms in the input file:
 
 ```plumed
 d1: DISTANCE_MATRIX GROUP=1-100
-n: NEIGHBOURS ARG=d1 NLOWEST=6
+n: NEIGHBORS ARG=d1 NLOWEST=6
 ```
 
 Alternatively, if you would like to use a CONTACT_MATRIX to do something similar you would do the following:
 
 ```plumed
 d1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.5}
-n: NEIGHBOURS ARG=c1 NHIGHEST=6
+n: NEIGHBORS ARG=c1 NHIGHEST=6
 ```
 
 This command is useful for implementing alternatives to the symmatry functions that are defined by the shortcuts
@@ -48,7 +48,7 @@ this coordination sphere contains only the four nearest atoms.  You can implemen
 
 ```plumed
 d1: DISTANCE_MATRIX GROUP=1-100 COMPONENTS
-n: NEIGHBOURS ARG=d1 NLOWEST=4 
+n: NEIGHBORS ARG=d1 NLOWEST=4 
 f: CUSTOM ARG=n,d1.x,d1.y,d1.z,d1.w VAR=w,x,y,z,r PERIODIC=NO FUNC=w*(((x+y+z)/r)^3+((x-y-z)/r)^3+((-x+y-z)/r)^3+((-x-y+z)/r)^3)
 ones: ONES SIZE=100
 ucv: MATRIX_VECTOR_FUNCTION ARG=f,ones

src/adjmat/TopologyMatrix.cpp

@@ -51,7 +51,7 @@ In this expression $s_1$ and $s_2$ are switching functions, while $\mathbf{r}_{l
 We then calculate the density for a grid of $M$ points along the vector connecting atom $i$ and atom $j$ using and find the maximum density on this grid using:
 
 $$
-\rho_{ij} = \max_{m \in M} \left[ \frac{M}{d_\textrm{max}} \sum_k f(\mathbf{r}_{ik}, \mathbf{r}_{ij}) \int_{(m-1)_d_{\textrm{max}}/M}^{ md_{\textrm{max}} /M } \textrm{d}x K\left( x - \mathbf{r}_{ks} \cdot \mathbf{r}_{ij}} / | \mathbf{r}_{ks} | \right) \right]
+\rho_{ij} = \max_{m \in M} \left[ \frac{M}{d_\textrm{max}} \sum_k f(\mathbf{r}_{ik}, \mathbf{r}_{ij}) \int_{(m-1)d_{\textrm{max}}/M}^{ md_{\textrm{max}} /M } \textrm{d}x K\left( x - \mathbf{r}_{ks} \cdot \mathbf{r}_{ij}} / | \mathbf{r}_{ks} | \right) \right]
 $$
 
 where $d_\textrm{max}$ is the `D_MAX` parameter of the switching function $s_3$ that appears in the next equation, $K$ is a kernal function and $s$ is used to represent a point in space that is $d_\textrm{max}$ from atom $j$ along the vector connecting atom $j$ to atom $i$.  

src/adjmat/TorsionsMatrix.cpp

@@ -50,7 +50,7 @@ around the vector connecting the corresponding atomic positions that are specifi
 
 You can also calculate a matrix of torsional angles between two different groups of molecules by using an input like the one below:
 
-```plmed
+```plumed
 pA: PLANE ATOMS1=1,2,3 ATOMS2=11,12,13 
 sA: VSTACK ARG=pA.x,pA.y pA.z
 pB: PLANE ATOMS1=21,22,23 ATOMS2=31,32,33 ATOMS3=41,42,43