diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp index feb4513306bf357d57110b7abaf1be552c6d53a7..fc99b888c7787278b91beb906cd678cac83f35d0 100644 --- a/src/colvar/ERMSD.cpp +++ b/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.