PLUMED: A portable plugin for free-energy calculations with molecular dynamics. - Massimiliano Bonomi; Davide Branduardi; Giovanni Bussi; Carlo Camilloni; Davide Provasi; Paolo Raiteri; Davide Donadio; Fabrizio Marinelli 002; Fabio Pietrucci; Ricardo A. Broglia; Michele Parrinello (Comput. Phys. Commun., 2009)

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. - Fabrizio Marinelli 002; Fabio Pietrucci; Alessandro Laio; Stefano Piana (PLoS Comput. Biol., 2009)

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. - Xevi Biarnés; Fabio Pietrucci; Fabrizio Marinelli 002; Alessandro Laio (Comput. Phys. Commun., 2012)

Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method. - Davide Branduardi; Fabrizio Marinelli 002; José D. Faraldo-Gómez (J. Comput. Chem., 2016)

A Matheuristic for the Design and Management of Multi-energy Systems. - Andrea Bartolini; Gabriele Comodi; Fabrizio Marinelli 002; Andrea Pizzuti; Roberto Rosetti (ICORES (Selected Papers), 2019)

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics. - Giacomo Fiorin; Fabrizio Marinelli 002; José D. Faraldo-Gómez (J. Comput. Chem., 2020)