\BOOKMARK [1][-]{section.1}{Introduction}{}% 1 \BOOKMARK [2][-]{subsection.1.1}{Overview}{section.1}% 2 \BOOKMARK [2][-]{subsection.1.2}{Collective variables}{section.1}% 3 \BOOKMARK [1][-]{section.2}{Step-by-step metadynamics calculations}{}% 4 \BOOKMARK [2][-]{subsection.2.1}{Compile Quantum ESPRESSO with PLUMED plugin}{section.2}% 5 \BOOKMARK [2][-]{subsection.2.2}{Running metadynamics in Quantum ESPRESSO}{section.2}% 6 \BOOKMARK [2][-]{subsection.2.3}{Units in the input and output files}{section.2}% 7 \BOOKMARK [2][-]{subsection.2.4}{Postprocessing}{section.2}% 8 \BOOKMARK [1][-]{section.3}{First worked example: SN2 reaction}{}% 9 \BOOKMARK [2][-]{subsection.3.1}{SN2 reaction in vacuum}{section.3}% 10 \BOOKMARK [2][-]{subsection.3.2}{Choice of CVs and simulation details}{section.3}% 11 \BOOKMARK [2][-]{subsection.3.3}{Metadynamics with Born-Oppenheimer molecular dynamics}{section.3}% 12 \BOOKMARK [3][-]{subsubsection.3.3.1}{Free energy reconstruction}{subsection.3.3}% 13 \BOOKMARK [1][-]{section.4}{Second worked example: H-H}{}% 14