Methods to derive free energies and kinetic rates

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Mean Forces

• MARINELLI F*, Faraldo-Gómez JD (2021). Force correction analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations. J. Chem. Theory Comput. vol. 17; p. 6775–6788. Link

Weighted histogram analysis and likelihood optimization

• MARINELLI F, Pietrucci F, Laio A, Piana S (2009). A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. PLOS COMPUT BIOL, vol. 5, ISSN: 1553-734X, doi: 10.1371/journal.pcbi.1000452, PDF, Link