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“…Such a guessed reaction coordinate, q(x), can be tested with the following procedure. The first step consists in calculating the free energy F (q), for instance by using umbrella sampling (Frenkel and Smit, 2002) or constrained molecular dynamics (Ciccotti, 1991). The free energy profile F (q) will possess minima at values of q typical for the stables states A and B and a barrier located at q = q * separating these two minima.…”

confidence: 99%

“…Such a guessed reaction coordinate, q(x), can be tested with the following procedure. The first step consists in calculating the free energy F (q), for instance by using umbrella sampling (Frenkel and Smit, 2002) or constrained molecular dynamics (Ciccotti, 1991). The free energy profile F (q) will possess minima at values of q typical for the stables states A and B and a barrier located at q = q * separating these two minima.…”

confidence: 99%

“…This method consists of two stages. First, the free energy is computed as a function of selected degrees of freedom describing the reaction from the initial to the final state (the reaction coordinate), for instance by biased sampling techniques [32,33,34]. This step is complemented with the calculation of a dynamical transmission coefficient, by starting short trajectories from the maximum of the free energy barrier.…”

confidence: 99%

“…This reaction coordinate can be any function λ(x) of phase space point x ≡ {r, p}, with r the particle coordinates and p the momenta. Next, the free energy F (λ) = −k B T ln(P (λ)) is calculated by determining the probability P (λ) to be at λ using, for instance, biased sampling techniques [17,18,19]. Here, k B is the Boltzmann constant and T is the temperature.…”

confidence: 99%