  To sample rare events, dissipation-corrected targeted molecular dynamics
(dcTMD) applies a constant velocity constraint along a one-dimensional reaction
coordinate $s$, which drives an atomistic system from an initial state into a
target state. Employing a cumulant approximation of Jarzynski's identity, the
free energy $\Delta G (s)$ is calculated from the mean external work and
dissipated work of the process. By calculating the friction coefficient $\Gamma
(s)$ from the dissipated work, in a second step the equilibrium dynamics of the
process can be studied by propagating a Langevin equation. While so far dcTMD
has been mostly applied to study the unbinding of protein-ligand complexes,
here its applicability to rare conformational transitions within a protein and
the prediction of their kinetics is investigated. As this typically requires
the introduction of multiple collective variables $\{x_j\}= \vec{x}$, a
theoretical framework is outlined to calculate the associated free energy
$\Delta G (\vec{x})$ and friction $\matrix{\Gamma}(\vec{x})$ from dcTMD
simulations along coordinate $s$. Adopting the $\alpha$-$\beta$ transition of
alanine dipeptide as well as the open-closed transition of T4 lysozyme as
representative examples, the virtues and shortcomings of dcTMD to predict
protein conformational transitions and the related kinetics are studied.
