Deployed f27746b with MkDocs version: 1.6.1

index.html

@@ -164,5 +164,5 @@ <h3 id="running-simulations-with-plumed-at-dipc"><a href="dipc/">Running simulat
 
 <!--
 MkDocs version : 1.6.1
-Build Date UTC : 2024-12-13 08:49:07.698744+00:00
+Build Date UTC : 2024-12-13 08:51:30.113360+00:00
 -->

metadynamics/metadynamics-with-Q/index.html

@@ -102,9 +102,9 @@ <h2 id="defining-native-contacts-q-as-collective-variable">Defining native conta
 <p>In order to understand how to implement Q as a collective variable in PLUMED
 one needs to understand how Q is defined:</p>
 <p>$$Q(X) = \frac{1}{N}\sum_{\left(i,i\right)}\frac{1}{1+exp\left[\beta \left(r_{ij}(X)-\lambda r^{0}_{ij}\right)\right]}$$</p>
-<p>where the sum runs over the $N$ pairs of native contacts <em>(i,j)</em>, $r_{ij}(X)$ is the 
-distance between <em>i</em> and <em>j</em> in configuration $X$, $r^{0}_{ij}$ is the distance between
-$i$ and $j$ in the native state, $\beta$ is a smoothing parameter taken to be 5 ${AA}^{-1}$ 
+<p>where the sum runs over the <em>N</em> pairs of native contacts <em>(i,j)</em>, <em>r</em>$<code>_{ij}</code>$<em>(X)</em> is the 
+distance between <em>i</em> and <em>j</em> in configuration <em>X</em>, $r^{0}<em>{ij}$ is the distance between
+_i</em> and <em>j</em> in the native state, $\beta$ is a smoothing parameter taken to be 5 ${AA}^{-1}$ 
 and the factor $\lambda$ accounts for fluctuations when the contact is formed, taken to be
 1.2.</p>