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@string{acmcs = {ACM Comp. Surv.}}

@string{acmtoplas = {ACM Trans. on Programming Languages and Systems}}

@string{addressvpi = {Blacksburg, VA  24061-0106}}

@string{as = {Applied Statistics}}

@article{plumed2,
  author={Gareth A. Tribello and Massimiliano Bonomi and Davide Branduardi and Carlo Camilloni and Giovanni Bussi},
  title={PLUMED 2: New feathers for an old bird},
  journal={Comput.~Phys.~Commun.},
  volume=185,
  number=2,
  pages={604--613},
  year=2014
}


@webpage{grometa}

@article{Vymetal:2011gv,
author = {Vym{\v e}tal, Ji{\v r}{\'\i} and Vondr{\'a}{\v s}ek, Ji{\v r}{\'\i}},
title = {{Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding}},
journal = {J. Phys. Chem. A},
year = {2011},
pages = {110930112611005},
}

@article{tribello-recon,
   author = {Gareth A. Tribello and Michele Ceriotti and Michele Parrinello}, 
   title = {{A self-learning algorithm for biased molecular dynamics}}, 
   volume = {107}, 
   number = {41}, 
   pages = {17509-17514}, 
   year = {2010}, 
   journal = {Proc. Natl. Acad. Sci. USA}
}

@article{field-cvs,
author = {Tribello, Gareth A. and Ceriotti, Michele and Parrinello, Michele},
title = {Using sketch-map coordinates to analyze and bias molecular dynamics simulations},
volume = {109},
number = {14}, 
pages = {5196-5201},
year = {2012},
doi = {10.1073/pnas.1201152109}, 
abstract ={When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.},
URL = {http://www.pnas.org/content/109/14/5196.abstract},
eprint = {http://www.pnas.org/content/109/14/5196.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

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title = {Exploring the free energy surfaces of clusters using reconnaissance metadynamics},
publisher = {AIP},
year = {2011},
volume = {135},
number = {11},
pages = {114109},
author = {Gareth A. Tribello and Jérôme Cuny and Hagai Eshet and Michele Parrinello},
journal = { J. Chem. Phys. }
}

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@article{piana08villin,
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year = {2006},
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abstract = {},
affiliation = {Univ Amsterdam, Amsterdam, Netherlands},
pages = {214A--214A},
year = {2007},
language = {English},
date-added = {2010-09-15 10:06:07 +0200},
date-modified = {2010-09-15 10:06:45 +0200},
pmid = {000243972401196},
}

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year = {2010},
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}

@article{Sahakyan:2011bn,
author = {Sahakyan, Aleksandr B and Vranken, Wim F and Cavalli, Andrea and Vendruscolo, Michele},
title = {{Structure-based prediction of methyl chemical shifts in proteins}},
journal = {J. Biomol. NMR},
year = {2011},
volume = {50},
number = {4},
pages = {331--346},
}

@article{PRL230602,
  title = {From Metadynamics to Dynamics},
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  url = {http://link.aps.org/doi/10.1103/PhysRevLett.111.230602},
  publisher = {American Physical Society}
}

@article{dellago-q6,
   author = "Lechner, Wolfgang and Dellago, Christoph",
   title = "Accurate determination of crystal structures based on averaged local bond order parameters",
   journal = "The Journal of Chemical Physics",
   year = "2008",
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   eid = 114707,
   pages = "-",
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   doi = "http://dx.doi.org/10.1063/1.2977970" 
}

@article {WCMS:WCMS31,
author = {Barducci, Alessandro and Bonomi, Massimiliano and Parrinello, Michele},
title = {Metadynamics},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
volume = {1},
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publisher = {John Wiley & Sons, Inc.},
issn = {1759-0884},
url = {http://dx.doi.org/10.1002/wcms.31},
doi = {10.1002/wcms.31},
pages = {826--843},
year = {2011},
}


@article {WCMS:WCMS1103,
author = {Sutto, Ludovico and Marsili, Simone and Gervasio, Francesco Luigi},
title = {New advances in metadynamics},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
volume = {2},
number = {5},
publisher = {John Wiley & Sons, Inc.},
issn = {1759-0884},
url = {http://dx.doi.org/10.1002/wcms.1103},
doi = {10.1002/wcms.1103},
pages = {771--779},
year = {2012},
}


@article{ct300297t,
author = {Deighan, Michael and Bonomi, Massimiliano and Pfaendtner, Jim},
title = {Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble},
journal = {Journal of Chemical Theory and Computation},
volume = {8},
number = {7},
pages = {2189-2192},
year = {2012},
doi = {10.1021/ct300297t},

URL = {http://pubs.acs.org/doi/abs/10.1021/ct300297t},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct300297t}
}

@article{Tiwary_jp504920s,
        Author = {Tiwary, Pratyush and Parrinello, Michele},
        Doi = {10.1021/jp504920s},
        Issn = {1520-5207},
        Journal = {The Journal of Physical Chemistry B},
        Month = {Jan},
        Number = {3},
        Pages = {736--742},
        Publisher = {American Chemical Society (ACS)},
        Title = {A Time-Independent Free Energy Estimator for Metadynamics},
        Url = {http://dx.doi.org/10.1021/jp504920s},
        Volume = {119},
        Year = {2015}
}

@article{Maragliano2006,
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Pages = {168-175},
Title = {A temperature-accelerated method for sampling free energy and determining reaction pathways in rare events simulations},
Volume = 426,
Year = 2006}

@article{AbramsJ2008,
Author = {Abrams, Jerry B. and Tuckerman, Mark E.},
Title = {{Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations}},
Journal = {J. Phys. Chem. B},
Year = {{2008}},
Volume = {{112}},
Number = {{49}},
Pages = {{15742-15757}},
Month = {{DEC 11}},
DOI = {{10.1021/jp805039u}}
}


@article{Ferrarotti2015,
        Author = {Marco Jacopo Ferrarotti and  Sandro Bottaro and  Andrea Perez-Villa and Giovanni Bussi},
        Journal = {J. Chem. Theory Comput.},
        Number = {1},
        Pages = {139--146},
        Title = {Accurate Multiple Time Step in Biased Molecular Simulations},
        Volume = {11},
        Year = {2015}
}

@article{Camilloni:2014iy,
author = {Camilloni, Carlo and Vendruscolo, Michele},
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journal = {J. Am. Chem. Soc.},
year = {2014},
volume = {136},
number = {25},
pages = {8982--8991},
}

@article{Camilloni:2013di,
author = {Camilloni, Carlo and Cavalli, Andrea and Vendruscolo, Michele},
title = {{Replica-Averaged Metadynamics}},
journal = {J. Chem. Theory Comput.},
year = {2013},
volume = {9},
number = {12},
pages = {5610--5617},
}

@article{Cavalli:2013jf,
author = {Cavalli, Andrea and Camilloni, Carlo and Vendruscolo, Michele},
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journal = {J. Chem. Phys.},
year = {2013},
volume = {138},
number = {9},
pages = {094112},
}

@article{Boomsma:2014br,
author = {Boomsma, Wouter and Lindorff-Larsen, Kresten and Ferkinghoff-Borg, Jesper},
title = {{Combining Experiments and Simulations Using the Maximum Entropy Principle}},
journal = {PLoS Comput. Biol.},
year = {2014},
volume = {10},
number = {2},
pages = {e1003406},
}

@article{huang2014improvement,
  title={Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods},
  author={Huang, Ming and Giese, Timothy J and Lee, Tai-Sung and York, Darrin M},
  journal={Journal of chemical theory and computation},
  volume={10},
  number={4},
  pages={1538--1545},
  year={2014},
  publisher={ACS Publications}
}

@article{gil2015enhanced,
  title={Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering},
  author={Gil-Ley, Alejandro and Bussi, Giovanni},
  journal={Journal of chemical theory and computation},
  volume={11},
  number={3},
  pages={1077--1085},
  year={2015},
  publisher={American Chemical Society}
}

@article{cremer1975general,
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  volume={97},
  number={6},
  pages={1354--1358},
  year={1975},
  publisher={ACS Publications}
}

@article{biarnes2007conformational,
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  author={Biarn{\'e}s, Xevi and Ardevol, Albert and Planas, Antoni and Rovira, Carme and Laio, Alessandro and Parrinello, Michele},
  journal={Journal of the American Chemical Society},
  volume={129},
  number={35},
  pages={10686--10693},
  year={2007},
  publisher={ACS Publications}
}



@Article{best2013,
   author="Best, R. B.  and Hummer, G.  and Eaton, W. A. ",
   title="{Native contacts determine protein folding mechanisms in atomistic simulations}",
   journal="Proc. Natl. Acad. Sci. U.S.A.",
   year="2013",
   volume="110",
   number="44",
   pages="17874--17879",
   doi = {10.1073/pnas.1311599110}, 
   URL = {http://www.pnas.org/content/110/44/17874.abstract},
   eprint = {http://www.pnas.org/content/110/44/17874.full.pdf+html}
}


@article{pbmetad,
author = {Jim Pfaendtner and Massimiliano Bonomi},
title = {Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics},
journal = {Journal of Chemical Theory and Computation},
volume = {11},
number = {11},
pages = {5062-5067},
year = {2015}
}

@article{marinelli2015ensemble,
        Author = {Marinelli, Fabrizio and Faraldo-G{\'o}mez, Jos{\'e} D},
        Date-Added = {2015-07-24 14:22:59 +0000},
        Date-Modified = {2015-09-27 11:05:20 +0000},
        Journal = {Biophys. J.},
        Number = {12},
        Pages = {2779-2782},
        Publisher = {Elsevier},
        Title = {Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions},
        Volume = {108},
        Year = {2015}}

@article{white2015designing,
        Author = {White, Andrew D and Dama, James F and Voth, Gregory A},
        Date-Added = {2015-07-24 14:23:23 +0000},
        Date-Modified = {2015-09-27 11:08:36 +0000},
        Journal = {J. Chem. Theory Comput.},
        Number = {6},
        Pages = {2451--2460},
        Publisher = {ACS Publications},
        Title = {Designing Free Energy Surfaces that Match Experimental Data with Metadynamics},
        Volume = {11},
        Year = {2015}}

@article{dama2014well,
        Author = {Dama, James F and Parrinello, Michele and Voth, Gregory A},
        Journal = {Phys. Rev. Lett.},
        Number = {24},
        Pages = {240602},
        Publisher = {APS},
        Title = {Well-Tempered Metadynamics Converges Asymptotically},
        Volume = {112},
        Year = {2014}}


@misc{gil2016empirical,
  title={Empirical corrections to the Amber RNA force field with Target Metadynamics},
  author={Gil-Ley, Alejandro and Bussi, Giovanni},
  journal={J. Chem. Theory Comput.},
  volume={12},
  number={6},
  pages={2790--2798},
  year={2016}
}


@article{perez2015atp,
  title={ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations},
  author={P{\'e}rez-Villa, Andrea and Darvas, Maria and Bussi, Giovanni},
  journal={Nucleic Acids Research},
  volume={43},
  number={18},
  pages={8725},
  year={2015},
  publisher={Oxford University Press}
}

@article{PratyushReweighting,
author = {Pratyush Tiwary and Michele Parrinello},
title = {A Time-Independent Free Energy Estimator for Metadynamics},
journal = {The Journal of Physical Chemistry B},
volume = {119}, 
number = {3},
pages = {736-742},
year = {2015},
doi = {10.1021/jp504920s},
    note ={PMID: 25046020},
        
URL = { 
        http://dx.doi.org/10.1021/jp504920s
        
},      
eprint = {
        http://dx.doi.org/10.1021/jp504920s

}

}

@article{bernd-path,
  title = {Path Finding on High-Dimensional Free Energy Landscapes},
  author = {D\'{\i}az Leines, Grisell and Ensing, Bernd},
  journal = {Phys. Rev. Lett.},
  volume = {109},
  issue = {2},
  pages = {020601},
  numpages = {4},
  year = {2012},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.109.020601},
  url = {http://link.aps.org/doi/10.1103/PhysRevLett.109.020601}
}


@article{smac-paper,
title = "Insight into the nucleation of urea crystals from the melt ",
journal = "Chemical Engineering Science ",
volume = "121",
number = "",
pages = "51 - 59",
year = "2015",
note = "2013 Danckwerts Special Issue on Molecular Modelling in Chemical Engineering ",
issn = "0009-2509",
doi = "http://dx.doi.org/10.1016/j.ces.2014.08.032",
url = "http://www.sciencedirect.com/science/article/pii/S0009250914004503",
author = "Federico Giberti and Matteo Salvalaglio and Marco Mazzotti and Michele Parrinello",
keywords = "Urea",
keywords = "Molecular dynamics",
keywords = "Nucleation",
keywords = "Free energy",
keywords = "Enhanced sampling",
keywords = "Well tempered metadynamics ",
abstract = "Abstract Obtaining molecular-level information regarding nucleation is an essential step towards a thorough comprehension of crystallization processes. In this work we investigate the nucleation of urea at the atomic scale using enhanced sampling Molecular Dynamics simulations. We show that by employing a set of suitably defined collective variables in a Well Tempered Metadynamics scheme it is possible to reversibly drive the system across the solid–liquid phase transition and to recover the associated free energy surface. Our study reveals the presence of an undiscovered metastable ordered structure competing with the experimental one during crystal nucleation, suggesting a non-classical mechanism for this process. "
}

@article{fcc-michele-1,
  title = {Solid-liquid interface free energy through metadynamics simulations},
  author = {Angioletti-Uberti, Stefano and Ceriotti, Michele and Lee, Peter D. and Finnis, Mike W.},
  journal = {Phys. Rev. B},
  volume = {81},
  issue = {12},
  pages = {125416},
  numpages = {11},
  year = {2010},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevB.81.125416},
  url = {http://link.aps.org/doi/10.1103/PhysRevB.81.125416}
}

@article{fcc-michele-2,
  title = {Solid-liquid interfacial free energy out of equilibrium},
  author = {Cheng, Bingqing and Tribello, Gareth A. and Ceriotti, Michele},
  journal = {Phys. Rev. B},
  volume = {92},
  issue = {18},
  pages = {180102},
  numpages = {5},
  year = {2015},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevB.92.180102},
  url = {http://link.aps.org/doi/10.1103/PhysRevB.92.180102}
}

@article{tribello-clustering,
  author = {Tribello, Gareth A. and Giberti, Federico and Sosso, Gabriele C. and Salvalaglio, Matteo and Parrinello, Michele},
  title = {Analyzing and Driving Cluster Formation in Atomistic Simulations},
  journal = {Journal of Chemical Theory and Computation},
  volume = {13},
  number = {3},
  pages = {1317-1327},
  year = {2017},
  doi = {10.1021/acs.jctc.6b01073},
  url = {http://dx.doi.org/10.1021/acs.jctc.6b01073}
}

@article{fede-grad,
author = {Giberti, Federico and Tribello, Gareth A. and Parrinello, Michele},
title = {Transient Polymorphism in NaCl},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {2526-2530},
pages = {null},
year = {2013},
doi = {10.1021/ct4002027},
URL = {http://pubs.acs.org/doi/abs/10.1021/ct4002027},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct4002027}
}

@article{gab-ice-kaolinite,
author = {Gabriele C. Sosso and Gareth A. Tribello and Andrea Zen and Philipp Pedevilla and Angelos Michaelides},
title = {Ice formation on kaolinite: Insights from molecular dynamics simulations},
journal = {The Journal of Chemical Physics},
volume = {145},
number = {21},
pages = {211927},
year = {2016},
doi = {10.1063/1.4968796},
URL = {http://dx.doi.org/10.1063/1.4968796},
eprint = {http://dx.doi.org/10.1063/1.4968796}
}

@article{wcsurface,
author = {Willard, Adam P. and Chandler, David},
title = {Instantaneous Liquid Interfaces},
journal = {The Journal of Physical Chemistry B},
volume = {114},
number = {5},
pages = {1954-1958},
year = {2010},
doi = {10.1021/jp909219k},
URL = {http://dx.doi.org/10.1021/jp909219k},
eprint = {http://dx.doi.org/10.1021/jp909219k}
}

@article{white2014efficient,
author = {White, Andrew D and Voth, Gregory A},
doi = {10.1021/ct500320c},
isbn = {1549-9618},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
pages = {3023--3030},
title = {{An Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data}},
url = {http://pubs.acs.org/doi/abs/10.1021/ct500320c},
volume = {10},
year = {2014}
}

@article{hocky2017cgds,
author = {Hocky, Glen M. and Dannenhoffer-Lafage, Thomas and Voth, Gregory A.},
title = {Coarse-Grained Directed Simulation},
journal = {Journal of Chemical Theory and Computation},
volume = {13},
number = {9},
pages = {4593-4603},
year = {2017},
doi = {10.1021/acs.jctc.7b00690},
}

@article{cunha2017unraveling,
  title={Unraveling Mg2+--RNA binding with atomistic molecular dynamics},
  author={Cunha, Richard A and Bussi, Giovanni},
  journal={RNA},
  volume={23},
  number={5},
  pages={628--638},
  year={2017},
  publisher={Cold Spring Harbor Lab}
}

@article{curuksu2009enhanced,
  title={Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach},
  author={Curuksu, Jeremy and Zacharias, Martin},
  journal={The Journal of chemical physics},
  volume={130},
  number={10},
  pages={03B610},
  year={2009},
  publisher={AIP}
}

@article{BerndAdaptivePath,
  Author = {Grisell Díaz Leines and Bernd Ensing},
  Journal = {Phys. Rev. Lett.},
  Month = {Feb},
  Pages = {020601},
  Title = {Path finding on high-dimensional free energy landscapes},
  Volume = {109},
  Year = {2012}
}

@article{Bonomi:2016ip,
author = {Bonomi, Massimiliano and Camilloni, Carlo and Cavalli, Andrea and Vendruscolo, Michele},
title = {{Metainference: A Bayesian inference method for heterogeneous systems.}},
journal = {Science Advances},
year = {2016},
volume = {2},
number = {1},
pages = {e1501177},
}

@article{Bonomi:2016ge,
author = {Bonomi, Massimiliano and Camilloni, Carlo and Vendruscolo, Michele},
title = {{Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics}},
journal = {Sci. Rep.},
year = {2016},
volume = {6},
pages = {31232},
}


@article{Lohr:2017gc,
author = {L{\"o}hr, Thomas and Jussupow, Alexander and Camilloni, Carlo},
title = {{Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide}},
journal = {J. Chem. Phys.},
year = {2017},
volume = {146},
number = {16},
pages = {165102--11},
}

@article{Camilloni:2015jf,
author = {Camilloni, Carlo and Vendruscolo, Michele},
title = {{Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles}},
journal = {Biochemistry},
year = {2015},
volume = {54},
number = {51},
pages = {7470--7476},
}

@article{Camilloni:2015ka,
author = {Camilloni, Carlo and Vendruscolo, Michele},
title = {{A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings}},
journal = {J. Phys. Chem. B},
year = {2015},
volume = {119},
number = {3},
pages = {653--661},
}

@article{Bonomi:2017dn,
author = {Bonomi, Massimiliano and Heller, Gabriella T and Camilloni, Carlo and Vendruscolo, Michele},
title = {{Principles of protein structural ensemble determination}},
journal = {Curr. Opin. Struct. Biol.},
year = {2017},
volume = {42},
pages = {106--116},
}

@article {Hanot113951,
author = {Hanot, Samuel and Bonomi, Massimiliano and Greenberg, Charles H and Sali, Andrej and Nilges, Michael and Vendruscolo, Michele and Pellarin, Riccardo},
title = {Multi-scale Bayesian modeling of cryo-electron microscopy density maps},
year = {2017},
volume = {},
number = {},
journal = {bioRxiv},
pages   = {doi: 10.1101/113951},
}

@article{cesari2016maxent,
  author    = {Andrea Cesari, Alejandro Gil-Ley and Giovanni Bussi},
  title     = {Combining Simulations and Solution Experiments as a Paradigm for {RNA} Force Field Refinement},
  journal   = {J Chem Theory Comput},
  year      = {2016},
  volume    = {12},
  number    = {12},
  pages     = {6192--6200},
  month     = {dec},
  doi       = {10.1021/acs.jctc.6b00944},
  publisher = {American Chemical Society ({ACS})},
}

@article{Bonomi:2017cc,
author = {Bonomi, Massimiliano and Camilloni, Carlo},
title = {{Integrative structural and dynamical biology with PLUMED-ISDB}},
journal = {Bioinformatics},
year = {2017},
volume = {33},
pages = {3999--4000},
}

@Article{Lelievre2007,
  author    = {Tony Leli{\`{e}}vre and Mathias Rousset and Gabriel Stoltz},
  title     = {Computation of free energy profiles with parallel adaptive dynamics},
  journal   = {The Journal of Chemical Physics},
  year      = {2007},
  volume    = {126},
  number    = {13},
  pages     = {134111},
  month     = {apr},
  doi       = {10.1063/1.2711185},
  publisher = {{AIP} Publishing},
}

@Article{Zheng2012,
  author    = {Lianqing Zheng and Wei Yang},
  title     = {Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering},
  journal   = {Journal of Chemical Theory and Computation},
  year      = {2012},
  volume    = {8},
  number    = {3},
  pages     = {810--823},
  month     = {mar},
  doi       = {10.1021/ct200726v},
  publisher = {American Chemical Society ({ACS})},
}

@Article{Fu2016,
  author    = {Haohao Fu and Xueguang Shao and Christophe Chipot and Wensheng Cai},
  title     = {Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations},
  journal   = {Journal of Chemical Theory and Computation},
  year      = {2016},
  volume    = {12},
  number    = {8},
  pages     = {3506--3513},
  month     = {aug},
  doi       = {10.1021/acs.jctc.6b00447},
  publisher = {American Chemical Society ({ACS})},
}

@Article{Lesage2016,
  author    = {Adrien Lesage and Tony Leli{\`{e}}vre and Gabriel Stoltz and J{\'{e}}r{\^{o}}me H{\'{e}}nin},
  title     = {Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method},
  journal   = {The Journal of Physical Chemistry B},
  year      = {2016},
  volume    = {121},
  number    = {15},
  pages     = {3676--3685},
  month     = {dec},
  doi       = {10.1021/acs.jpcb.6b10055},
  publisher = {American Chemical Society ({ACS})},
}

%% VES - added by OV
@book{Boyd-Chebyshev,
	Address = {New York},
	Author = {Boyd, John P.},
	Doi = {10.1007/b97441},
	Edition = {2nd},
	Publisher = {Dover Publications},
	Title = {Chebyshev and Fourier Spectral Methods},
	Year = {2001}}

%% VES - added by OV
@article{McCarty-PRL-2015,
        Author = {McCarty, James and Valsson, Omar and Tiwary, Pratyush and Parrinello, Michele},
        Doi = {10.1103/physrevlett.115.070601},
        Journal = {Phys. Rev. Lett.},
        Number = {7},
        Pages = {070601},
        Publisher = {American Physical Society (APS)},
        Title = {Variationally Optimized Free-Energy Flooding for Rate Calculation},
        Url = {http://dx.doi.org/10.1103/PhysRevLett.115.070601},
        Volume = {115},
        Year = {2015}
}

%% VES - added by OV
@article{Valsson-JCTC-2015,
	Author = {Valsson, Omar and Parrinello, Michele},
	Journal = {J. Chem. Theory Comput.},
	Number = {5},
	Pages = {1996--2002},
	Title = {{Well-Tempered Variational Approach to Enhanced Sampling}},
	Volume = {11},
        Doi = {10.1021/acs.jctc.5b00076},
        Url = {http://doi.org/10.1021/acs.jctc.5b00076},
	Year = {2015}
}

%% VES - added by OV
@article{Valsson-PRL-2014,
	Author = {Valsson, Omar and Parrinello, Michele},
	Doi = {10.1103/physrevlett.113.090601},
	Journal = {Phys. Rev. Lett.},
	Number = {9},
	Pages = {090601},
	Publisher = {American Physical Society (APS)},
	Title = {Variational Approach to Enhanced Sampling and Free Energy Calculations},
	Url = {http://dx.doi.org/10.1103/PhysRevLett.113.090601},
	Volume = {113},
	Year = {2014}
}

%% VES - added by OV
@article{Robbins-AnnMathStat-1951,
	Author = {Robbins, Herbert and Monro, Sutton},
	Doi = {10.1214/aoms/1177729586},
	Url = {http://doi.org/10.1214/aoms/1177729586},
	Journal = {Ann. Math. Stat.},
	Number = {3},
	Pages = {400--407},
	Publisher = {Institute of Mathematical Statistics},
	Title = {A Stochastic Approximation Method},
	Volume = {22},
	Year = {1951}
}

%% VES - added by OV
@incollection{Bach-NIPS-2013,
	Author = {Bach, Francis and Moulines, Eric},
	Booktitle = {Advances in Neural Information Processing Systems 26},
	Editor = {C.J.C. Burges and L. Bottou and M. Welling and Z. Ghahramani and K.Q. Weinberger},
	Pages = {773--781},
	Publisher = {Curran Associates, Inc., Red Hook, NY},
	Title = {Non-strongly-convex smooth stochastic approximation with convergence rate O(1/n)},
  Url = {http://papers.nips.cc/paper/4900-non-strongly-convex-smooth-stochastic-approximation-with-convergence-rate-o1n.pdf},
	Year = {2013}
}
	
%% VES - added by OV
@article{Pettitt-JCP-1986,
	title={Alkali halides in water: Ion--solvent correlations and ion--ion potentials of mean force at infinite dilution},
	author={Pettitt, B Montgomery and Rossky, Peter J},
	journal={The Journal of chemical physics},
	volume={84},
	number={10},
	pages={5836--5844},
	year={1986},
	publisher={AIP}
}

%% VES - added by OV
@article{Price-JCP-2004,
	title={A modified TIP3P water potential for simulation with Ewald summation},
	author={Price, Daniel J and Brooks III, Charles L},
	journal={The Journal of chemical physics},
	volume={121},
	number={20},
	pages={10096--10103},
	year={2004},
	publisher={AIP}
}

%% VES - added by OV
@article{Shaffer-PNAS-2016,
        Author = {Shaffer, Patrick and Valsson, Omar and Parrinello, Michele},
        Doi = {10.1073/pnas.1519712113},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Number = {5},
        Pages = {1150--1155},
        Title = {Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin},
        Url = {http://dx.doi.org/10.1073/pnas.1519712113},
        Volume = {113},
        Year = {2016}
}

%% VES - added by MI
@article{Invernizzi2019vesdeltaf,
  Title = {Making the Best of a Bad Situation: a Multiscale Approach to Free Energy Calculation},
  Author = {Invernizzi, Michele and Parrinello, Michele},
	Journal = {J. Chem. Theory Comput.},
	Pages = {2187--2194},
	Number = {4},
	Volume = {15},
  Year = {2019},
  Doi = {10.1021/acs.jctc.9b00032},
  Url = {http://doi.org/10.1021/acs.jctc.9b00032}
}

%% VES - added by PP
@article{Piaggi-PRL-2019,
  title = {Multithermal-Multibaric Molecular Simulations from a Variational Principle},
  author = {Piaggi, Pablo M. and Parrinello, Michele},
  journal = {Phys. Rev. Lett.},
  volume = {122},
  issue = {5},
  pages = {050601},
  numpages = {6},
  year = {2019},
  month = {Feb},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.122.050601},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.122.050601}
}

%% VES - added by PP
@article{Piaggi-JCP-2019,
  title={Calculation of phase diagrams in the multithermal-multibaric ensemble},
  author={Piaggi, Pablo M and Parrinello, Michele},
  journal={The Journal of chemical physics},
  volume={150},
  number={24},
  pages={244119},
  year={2019},
  publisher={AIP Publishing LLC}
}

@article{Berg-PRL-1992,
  title = {Multicanonical ensemble: A new approach to simulate first-order phase transitions},
  author = {Berg, Bernd A. and Neuhaus, Thomas},
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  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.68.9},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.68.9}
}

@article{Okumura-CPL-2004,
  title = "Molecular dynamics simulations in the multibaric–multithermal ensemble",
  journal = "Chemical Physics Letters",
  volume = "391",
  number = "4",
  pages = "248 - 253",
  year = "2004",
  issn = "0009-2614",
  doi = "https://doi.org/10.1016/j.cplett.2004.04.073",
  url = "http://www.sciencedirect.com/science/article/pii/S0009261404006347",
  author = "Hisashi Okumura and Yuko Okamoto"
}

@Article{Zhao2017,
  author    = {Tanfeng Zhao and Haohao Fu and Tony Leli{\`{e}}vre and Xueguang Shao and Christophe Chipot and Wensheng Cai},
  title     = {The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations},
  journal   = {Journal of Chemical Theory and Computation},
  year      = {2017},
  volume    = {13},
  number    = {4},
  pages     = {1566--1576},
  doi       = {10.1021/acs.jctc.7b00032},
  publisher = {American Chemical Society ({ACS})}
}

%% FaMetaD - added by OV
@article{Wang-JCP-2018,
         title={Frequency adaptive metadynamics for the calculation of rare-event kinetics},
         volume={149},
         ISSN={1089-7690},
         url={http://dx.doi.org/10.1063/1.5024679},
         DOI={10.1063/1.5024679},
         number={7},
         journal={The Journal of Chemical Physics},
         publisher={AIP Publishing},
         author={Wang, Yong and Valsson, Omar and Tiwary, Pratyush and Parrinello, Michele and Lindorff-Larsen, Kresten},
         year={2018},
         month={Aug},
         pages={072309}
}

@article{Capelli:2018jt,
author = {Capelli, Riccardo and Tiana, Guido and Camilloni, Carlo},
title = {{An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations}},
journal = {J. Chem. Phys.},
year = {2018},
volume = {148},
number = {18},
pages = {184114},
month = may
}

@article{pipolo2017navigating,
  title = {Navigating at Will on the Water Phase Diagram},
  author = {Pipolo, S. and Salanne, M. and Ferlat, G. and Klotz, S. and Saitta, A. M. and Pietrucci, F.},
  journal = {Phys. Rev. Lett.},
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  issue = {24},
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  numpages = {5},
  year = {2017},
  month = {Dec},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.119.245701},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.119.245701}
}

@article{gallet2013structural,
author = {Gallet,Grégoire A.  and Pietrucci,Fabio },
title = {Structural cluster analysis of chemical reactions in solution},
journal = {The Journal of Chemical Physics},
volume = {139},
number = {7},
pages = {074101},
year = {2013},
doi = {10.1063/1.4818005}
}

@article{dimer-metad,
author = {Marco Nava and Ferruccio Palazzesi and Claudio Perego and Michele Parrinello },
title = {Dimer Metadynamics},
journal = {Journal of Chemical Theory and Computation},
volume = {13},
number = {2},
pages = {425-430},
year = {2017},
doi = {10.1021/acs.jctc.6b00691}
}

@article{MorishitaLogMFD,
author = {Morishita, T. and Itoh, S. G. and Okumura, H. and Mikami, M.},
title = {Free-energy calculation via mean-force dynamics using a logarithmic energy landscape},
journal = {Physical Review E},
volume = {85},
pages = {066702},
year = {2012},
doi = {10.1103/PhysRevE.85.066702}
}

@article{MorishitaLogPD,
author = {Morishita, T. and Yonezawa, Y and Ito, A. M.},
title = {Free energy reconstruction from logarithmic mean-force dynamics using multiple nonequilibrium trajectories},
journal = {Journal of Chemical Theory and Computation},
volume = {13},
pages = {3106},
year = {2017},
doi = {10.1021/acs.jctc.7b00252}
}

@article{MorishitaVsLogMFD,
author = {Morishita, T. and Nakamura, T and Shinoda, W and Ito, A. M.},
title = {Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction},
journal = {Chemical Physics Letter},
volume = {706},
pages = {633},
year = {2018}
}

@article{Amirkulova2019Recent,
author = {Amirkulova, Dilnoza and White, Andrew D.},
title = {Recent advances in maximum entropy biasing techniques for molecular dynamics},
journal = {arXiv preprint arXiv:1902.02252},
year = {2019}
}

@article{Niebling:2014jy,
author = {Niebling, Stephan and Bj{\"o}rling, Alexander and Westenhoff, Sebastian},
title = {{MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins}},
journal = {J Appl Crystallogr},
year = {2014},
volume = {47},
number = {4},
pages = {1190--1198},
month = aug
}

@article{Valentini:2015ki,
author = {Valentini, Erica and Kikhney, Alexey G and Previtali, Gianpietro and Jeffries, Cy M and Svergun, Dmitri I},
title = {{SASBDB, a repository for biological small-angle scattering data.}},
journal = {Nucleic Acids Res},
year = {2015},
volume = {43},
number = {Database issue},
pages = {D357--63},
month = jan
}

@article{Paissoni:2019ee,
author = {Paissoni, Cristina and Jussupow, Alexander and Camilloni, Carlo},
title = {{Martini bead form factors for nucleic acids and their application in the refinement of protein{\textendash}nucleic acid complexes against SAXS data}},
journal = {J Appl Crystallogr},
year = {2019},
volume = {52},
number = {2},
pages = {394--402},
month = apr
}

%maze
@article{RydzewskiMaze,
  title={Finding Multiple Reaction Pathways of Ligand Unbinding},
  author={Rydzewski, J and Valsson, O},
  journal={arXiv: 1808.08089},
  year={2018},
  url={https://arxiv.org/abs/1808.08089}
}

@article{Chen2018,
  title = {{ELF}: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines},
  author = {Haochuan Chen and Haohao Fu and Xueguang Shao and Christophe Chipot and Wensheng Cai},
  journal = {Journal of Chemical Information and Modeling},
  volume = {58},
  pages = {1315--1318},
  year = {2018},
  month = {Jun},
  publisher = {American Chemical Society ({ACS})},
  doi = {10.1021/acs.jcim.8b00115},
  url = {https://pubs.acs.org/doi/10.1021/acs.jcim.8b00115}
}

@article{bussi2015free,
  title={Free-energy calculations with metadynamics: Theory and practice},
  author={Bussi, Giovanni and Branduardi, Davide and others},
  journal={Rev. Comput. Chem},
  volume={28},
  pages={1--49},
  year={2015},
  publisher={Wiley Online Library}
}

@article{Giberti_jp16100,
  author = {Giberti, F. and Cheng, B. and Tribello, G. A. and Ceriotti, M.},
  title = {Iterative Unbiasing of Quasi-Equilibrium Sampling},
  journal = {Journal of Chemical Theory and Computation},
  volume = {16},
  number = {1},
  pages = {100-107},
  year = {2020},
  doi = {10.1021/acs.jctc.9b00907},
  note ={PMID: 31743021},
  URL = { 
          https://doi.org/10.1021/acs.jctc.9b00907

  },
  eprint = { 
          https://doi.org/10.1021/acs.jctc.9b00907

  }
}

@article{Hovan2019,
  author = {Hovan, Ladislav and Comitani, Federico and Gervasio, Francesco L},
  doi = {10.1021/acs.jctc.8b00563},
  issn = {1549-9618},
  journal = {Journal of Chemical Theory and Computation},
  number = {1},
  pages = {25--32},
  publisher = {American Chemical Society},
  title = {{An Optimal Metric for the Path Collective Variables}},
  volume = {15},
  year = {2019}
}

@article{Hartmann-FISST-2019,
  title={Infinite Switch Simulated Tempering in Force (FISST)},
  author={Hartmann, Michael J and Singh, Yuvraj and Vanden-Eijnden, Eric and Hocky, Glen M},
  journal={arXiv:1910.14064},
  year={2019},
}

%% OPES
@article{Invernizzi2020rethinking,
  title = {Rethinking Metadynamics: From Bias Potentials to Probability Distributions},
  author = {Invernizzi, Michele and Parrinello, Michele},
  journal = {The Journal of Physical Chemistry Letters},
  doi = {10.1021/acs.jpclett.0c00497},
  arxivId = {1909.07250},
  issn = {1948-7185},
  url = {https://pubs.acs.org/doi/10.1021/acs.jpclett.0c00497},
  month = {apr},
  number = {7},
  pages = {2731--2736},
  volume = {11},
  year = {2020}
}

@article{Pietrucci2017review,
  author = {Pietrucci, Fabio},
  doi = {10.1016/j.revip.2017.05.001},
  issn = {24054283},
  journal = {Reviews in Physics},
  pages = {32--45},
  publisher = {Elsevier B.V.},
  title = {{Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead}},
  url = {https://doi.org/10.1016/j.revip.2017.05.001},
  volume = {2},
  year = {2017}
}


@article{limongelli2013funnel,
  title={Funnel metadynamics as accurate binding free-energy method},
  author={Limongelli, Vittorio and Bonomi, Massimiliano and Parrinello, Michele},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={16},
  pages={6358--6363},
  year={2013},
  publisher={National Acad Sciences}
}

@article{raniolo2020ligand,
  title={Ligand binding free-energy calculations with funnel metadynamics},
  author={Raniolo, Stefano and Limongelli, Vittorio},
  journal={Nature Protocols},
  volume={15},
  number={9},
  pages={2837--2866},
  year={2020},
  publisher={Nature Publishing Group}
}

@Comment{jabref-meta: databaseType:bibtex;}
