Deployed 709ca5a 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 08:37:01.124416+00:00
+Build Date UTC : 2024-12-13 08:41:52.970245+00:00
 -->

metadynamics/metadynamics-with-Q/index.html

@@ -102,10 +102,10 @@ <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 $(i,j)$, $r_{ij}(X)$ is the 
-distance between $i$ and $j$ 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 $\AA ^{-1}$ and
-the factor $\lambda$ accounts for fluctuations when the contact is formed, taken to be
+<p>where the sum runs over the $N$ pairs of native contacts $<code>(i,j)</code>$, $<code>r_{ij}(X)</code>$ is the 
+distance between $<code>i</code>$ and $<code>j</code>$ in configuration $<code>X</code>$, $<code>r^{0}_{ij}</code>$ is the distance between
+&i; and &j; in the native state, $<code>\beta</code>$ is a smoothing parameter taken to be 5 $<code>\AA ^{-1}</code>$ 
+and the factor $<code>\lambda</code>$ accounts for fluctuations when the contact is formed, taken to be
 1.2.</p>
 
             </div>