Publication on metadynamics


  • A Laio, M Parrinello,
    Escaping free-energy minima
     PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF, 99, 12562 (2002)

  • R Martonak, A Laio, M Parrinello,
    Predicting crystal structures: The Parrinello-Rahman method revisited
     PHYSICAL REVIEW LETTERS, 90, 075503 (2003)
    Here the approach is extended for studying structural transformations, using the six components of the simulation box as collective variables.

  • M Iannuzzi, A Laio, M Parrinello,
    Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics
     PHYSICAL REVIEW LETTERS, 90, 238302 (2003)
    The approach is combined with Car-Parrinello molecular dynamics in order to study chemical reaction. The continuous (lagrangean) version of the algorithm is also introduced.

  • C Micheletti, A Laio, M Parrinello,
    Reconstructing the density of states by history-dependent metadynamics
     PHYSICAL REVIEW LETTERS, 92, 170601 (2004)
    The approach is used for reconstructing the density of states. First analysis of the error/accuracy.

  • A Laio, A Rodriguez-Fortea, FL Gervasio, M Ceccarelli, M Parrinello,
    Assessing the accuracy of metadynamics
     JOURNAL OF PHYSICAL CHEMISTRY B, 109, 6714 (2005)

  • S Piana, A Laio,
    A bias-exchange approach to protein folding
     JOURNAL OF PHYSICAL CHEMISTRY B, 111, 4553 (2007)

  • G Bussi, FL Gervasio, A Laio, M Parrinello,
    Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
     JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128, 13435 (2006)

  • G Bussi, A Laio, M Parrinello,
    Equilibrium free energies from nonequilibrium metadynamics
     PHYSICAL REVIEW LETTERS, 96, 090601 (2006)

  • P Raiteri, A Laio, FL Gervasio, C Micheletti, M Parrinello,
    Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
     JOURNAL OF PHYSICAL CHEMISTRY B, 110, 3533 (2006)

  • A Laio, FL Gervasio,
    Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
     REPORTS ON PROGRESS IN PHYSICS, 71, 126601 (2008)

  • Y Crespo, A Laio, GE Santoro, E Tosatti,
    Calculating thermodynamics properties of quantum systems by a non-Markovian Monte Carlo procedure
     PHYSICAL REVIEW E, 80, 015702 (2009)

  • C Michel, A Laio, A Milet,
    Tracing the Entropy along a Reactive Pathway: The Energy As a Generalized Reaction Coordinate
     JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5, 2193 (2009)

  • L Mones, P Kulhanek, I Simon, A Laio, M Fuxreiter,
    The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions
     JOURNAL OF PHYSICAL CHEMISTRY B, 113, 7867 (2009)

  • F Marinelli, F Pietrucci, A Laio, S Piana,
    A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
     PLOS COMPUTATIONAL BIOLOGY, 5, e1000452 (2009)

  • Y Crespo, F Marinelli, F Pietrucci, A Laio,
    Metadynamics convergence law in a multidimensional system
     PHYSICAL REVIEW E, 81, 055701 (2010)

  • P Cossio, F Marinelli, A Laio, F Pietrucci,
    Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model
     JOURNAL OF PHYSICAL CHEMISTRY B, 114, 3259 (2010)

  • D Granata, C Camilloni, M Vendruscolo, A Laio,
    Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics
     PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF, 110, 6817 (2013)

  • F Baftizadeh, F Pietrucci, X Biarnes, A Laio,
    Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-beta
     PHYSICAL REVIEW LETTERS, 110, 168103 (2013)

  • F Baftizadeh, X Biarnes, F Pietrucci, F Affinito, A Laio,
    Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
     JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134, 3886 (2012)

  • X Biarnes, F Pietrucci, F Marinelli, A Laio,
    METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations
     COMPUTER PHYSICS COMMUNICATIONS, 183, 203 (2012)