Merge remote-tracking branch 'origin/v2.4' into v2.4-ves

src/colvar/DRMSD.cpp

@@ -45,7 +45,7 @@ often cheaper and easier to calculate the distances between all the pairs of ato
 between the two structures, \f$\mathbf{X}^a\f$ and \f$\mathbf{X}^b\f$ can then be measured as:
 
 \f[
-d(\mathbf{X}^A, \mathbf{X}^B) = \frac{1}{N(N-1)} \sum_{i \ne j} [ d(\mathbf{x}_i^a,\mathbf{x}_j^a) - d(\mathbf{x}_i^b,\mathbf{x}_j^b) ]^2
+d(\mathbf{X}^A, \mathbf{X}^B) = \sqrt{\frac{1}{N(N-1)} \sum_{i \ne j} [ d(\mathbf{x}_i^a,\mathbf{x}_j^a) - d(\mathbf{x}_i^b,\mathbf{x}_j^b) ]^2}
 \f]
 
 where \f$N\f$ is the number of atoms and \f$d(\mathbf{x}_i,\mathbf{x}_j)\f$ represents the distance between

src/colvar/ERMSD.cpp

@@ -55,12 +55,13 @@ eRMSD measures the distance between structures by considering only the relative
 
 2. Calculate all pairwise distance vectors \f$ \vec{r}_{i,j} \f$ among base centers.
 
-3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where \f$ a=b=5 \AA, c= 3 \AA\f$. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
+3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where  a=b=5 \AA, c= 3 \AA. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
 
 4. Calculate the G vectors
 
 \f[
-\vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times \Theta(\tilde{r}_{cutoff}-\tilde{r})
+\vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times
+\frac{\Theta(\tilde{r}_{cutoff}-\tilde{r})}{\gamma}
 \f]
 
 Here, \f$ \gamma = \pi/\tilde{r}_{cutoff}\f$ and \f$ \Theta \f$ is the Heaviside step function. The default cutoff is set to 2.4.

user-doc/tutorials/belfast-7.txt

@@ -22,7 +22,7 @@ In PT, exchanges are usually attempted between adjacent temperatures
 with the following acceptance probability:
 
 \f[
-p(i \rightarrow j) = min \{ 1,\Delta_{i,j}^{PT} \},
+p(i \rightarrow j) = min \{ 1,e^{\Delta_{i,j}^{PT}} \},
 \f]
 
 with