Variational Metadynamics

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Publications

Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations

Author(s): Riccardo Capelli, Anna Bochicchio, GiovanniMaria Piccini, Rodrigo Casasnovas, Paolo Carloni, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/5, 2019, Page(s) 3354-3361, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00118

The role of water in host-guest interaction

Author(s): Valerio Rizzi, Luigi Bonati, Narjes Ansari, Michele Parrinello
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20310-0

Accurate Quantum Chemical Free Energies at Affordable Cost

Author(s): GiovanniMaria Piccini, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 10/13, 2019, Page(s) 3727-3731, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.9b01301

Path integral molecular dynamics for fermions: Alleviating the sign problem with the Bogoliubov inequality

Author(s): Barak Hirshberg, Michele Invernizzi, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 152/17, 2020, Page(s) 171102, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0008720

Collective variables for the study of crystallisation

Author(s): Tarak Karmakar, Michele Invernizzi, Valerio Rizzi, Michele Parrinello
Published in: Molecular Physics, 2021, Page(s) e1893848, ISSN 0026-8976
Publisher: Taylor & Francis
DOI: 10.1080/00268976.2021.1893848

Ab initio phase diagram and nucleation of gallium

Author(s): Haiyang Niu, Luigi Bonati, Pablo M. Piaggi, Michele Parrinello
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16372-9

Metadynamics of Paths

Author(s): Davide Mandelli, Barak Hirshberg, Michele Parrinello
Published in: Physical Review Letters, Issue 125/2, 2020, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.125.026001

Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables

Author(s): Z. Faidon Brotzakis, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/2, 2018, Page(s) 1393-1398, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b00827

Calculation of phase diagrams in the multithermal-multibaric ensemble

Author(s): Pablo M. Piaggi, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 150/24, 2019, Page(s) 244119, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5102104

Improving collective variables: The case of crystallization

Author(s): Yue-Yu Zhang, Haiyang Niu, GiovanniMaria Piccini, Dan Mendels, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 150/9, 2019, Page(s) 094509, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5081040

Unified Approach to Enhanced Sampling

Author(s): Michele Invernizzi, Pablo M. Piaggi, Michele Parrinello
Published in: Physical Review X, Issue 10/4, 2020, ISSN 2160-3308
Publisher: American Physical Society
DOI: 10.1103/physrevx.10.041034

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

Author(s): Matteo Salvalaglio, Pratyush Tiwary, Giovanni Maria Maggioni, Marco Mazzotti, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 145/21, 2016, Page(s) 211925, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.4966265

Entropy based fingerprint for local crystalline order

Author(s): Pablo M. Piaggi, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 147/11, 2017, Page(s) 114112, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.4998408

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations

Author(s): Rodrigo Casasnovas, Vittorio Limongelli, Pratyush Tiwary, Paolo Carloni, Michele Parrinello
Published in: Journal of the American Chemical Society, Issue 139/13, 2017, Page(s) 4780-4788, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.6b12950

Collective Variables from Local Fluctuations

Author(s): Dan Mendels, GiovanniMaria Piccini, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 9/11, 2018, Page(s) 2776-2781, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.8b00733

Molecular dynamics simulations of liquid silica crystallization

Author(s): Haiyang Niu, Pablo M. Piaggi, Michele Invernizzi, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 115/21, 2018, Page(s) 5348-5352, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1803919115

Controversial Effects of D-Amino Acid Oxidase Activator (DAOA)/G72 on D-Amino Acid Oxidase (DAO) Activity in Human Neuronal, Astrocyte and Kidney Cell Lines: The N-methyl D-aspartate (NMDA) Receptor Hypofunction Point of View

Author(s): Vinita Jagannath, Zacharias Faidon Brotzakis, Michele Parrinello, Susanne Walitza, Edna Grünblatt
Published in: Frontiers in Molecular Neuroscience, Issue 10, 2017, ISSN 1662-5099
Publisher: Frontiers Research Foundation
DOI: 10.3389/fnmol.2017.00342

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling

Author(s): Yi Isaac Yang, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 14/6, 2018, Page(s) 2889-2894, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b00231

A variational conformational dynamics approach to the selection of collective variables in metadynamics

Author(s): James McCarty, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 147/20, 2017, Page(s) 204109, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.4998598

Chemical potential calculations in non-homogeneous liquids

Author(s): Claudio Perego, Omar Valsson, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 149/7, 2018, Page(s) 072305, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5024631

Conformational Entropy as Collective Variable for Proteins

Author(s): Ferruccio Palazzesi, Omar Valsson, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 8/19, 2017, Page(s) 4752-4756, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.7b01770

Frequency adaptive metadynamics for the calculation of rare-event kinetics

Author(s): Yong Wang, Omar Valsson, Pratyush Tiwary, Michele Parrinello, Kresten Lindorff-Larsen
Published in: The Journal of Chemical Physics, Issue 149/7, 2018, Page(s) 072309, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5024679

Quantum Symmetry from Enhanced Sampling Methods

Author(s): J. Runeson, M. Nava, M. Parrinello
Published in: Physical Review Letters, Issue 121/14, 2018, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.121.140602

Predicting polymorphism in molecular crystals using orientational entropy

Author(s): Pablo M. Piaggi, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 115/41, 2018, Page(s) 10251-10256, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1811056115

Combining Metadynamics and Integrated Tempering Sampling

Author(s): Yi Isaac Yang, Haiyang Niu, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 9/22, 2018, Page(s) 6426-6430, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.8b03005

Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics

Author(s): Luigi Bonati, Michele Parrinello
Published in: Physical Review Letters, Issue 121/26, 2018, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.121.265701

Folding a small protein using harmonic linear discriminant analysis

Author(s): Dan Mendels, Giovannimaria Piccini, Z. Faidon Brotzakis, Yi I. Yang, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 149/19, 2018, Page(s) 194113, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5053566

Accelerating the Calculation of Protein–Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables

Author(s): Z. Faidon Brotzakis, Vittorio Limongelli, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/1, 2018, Page(s) 743-750, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b00934

Prion protein β 2– α 2 loop conformational landscape

Author(s): Enrico Caldarulo, Alessandro Barducci, Kurt Wüthrich, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 114/36, 2017, Page(s) 9617-9622, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1712155114

Neural networks-based variationally enhanced sampling

Author(s): Luigi Bonati, Yue-Yu Zhang, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 116/36, 2019, Page(s) 17641-17647, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1907975116

Enhanced Sampling of Transition States

Author(s): Jayashrita Debnath, Michele Invernizzi, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/4, 2019, Page(s) 2454-2459, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b01283

Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential

Author(s): Tarak Karmakar, Pablo M. Piaggi, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/12, 2019, Page(s) 6923-6930, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00795

Identifying Slow Molecular Motions in Complex Chemical Reactions

Author(s): GiovanniMaria Piccini, Daniela Polino, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 8/17, 2017, Page(s) 4197-4200, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.7b01889

Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis

Author(s): Valerio Rizzi, Dan Mendels, Emilia Sicilia, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/8, 2019, Page(s) 4507-4515, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00358

Path integral molecular dynamics for bosons

Author(s): Barak Hirshberg, Valerio Rizzi, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 116/43, 2019, Page(s) 21445-21449, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1913365116

The Onset of Dehydrogenation in Solid Ammonia Borane: An Ab Initio Metadynamics Study

Author(s): Valerio Rizzi, Daniela Polino, Emilia Sicilia, Nino Russo, Michele Parrinello
Published in: Angewandte Chemie International Edition, Issue 58/12, 2019, Page(s) 3976-3980, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201900134

Metadynamics with Discriminants: A Tool for Understanding Chemistry

Author(s): GiovanniMaria Piccini, Dan Mendels, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 14/10, 2018, Page(s) 5040-5044, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b00634

Microscopic description of acid–base equilibrium

Author(s): Emanuele Grifoni, GiovanniMaria Piccini, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 116/10, 2019, Page(s) 4054-4057, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1819771116

A Cannibalistic Approach to Grand Canonical Crystal Growth

Author(s): Tarak Karmakar, Pablo M. Piaggi, Claudio Perego, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 14/5, 2018, Page(s) 2678-2683, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b00191

Making the Best of a Bad Situation: A Multiscale Approach to Free Energy Calculation

Author(s): Michele Invernizzi, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 15/4, 2019, Page(s) 2187-2194, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b00032

Temperature Dependence of Homogeneous Nucleation in Ice

Author(s): Haiyang Niu, Yi Isaac Yang, Michele Parrinello
Published in: Physical Review Letters, Issue 122/24, 2019, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.122.245501

Searching for Entropically Stabilized Phases: The Case of Silver Iodide

Author(s): Dan Mendels, James McCarty, Pablo M. Piaggi, Michele Parrinello
Published in: The Journal of Physical Chemistry C, Issue 122/3, 2018, Page(s) 1786-1790, ISSN 1932-7447
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcc.7b11002

Multithermal-Multibaric Molecular Simulations from a Variational Principle

Author(s): Pablo M. Piaggi, Michele Parrinello
Published in: Physical Review Letters, Issue 122/5, 2019, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.122.050601

Communication: Role of explicit water models in the helix folding/unfolding processes

Author(s): Ferruccio Palazzesi, Matteo Salvalaglio, Alessandro Barducci, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 145, 2016, Page(s) 121101, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.4963340

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling

Author(s): Patrick Shaffer, Omar Valsson, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 12/12, 2016, Page(s) 5751-5757, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.6b00786

Chemical potential calculations in dense liquids using metadynamics

Author(s): C. Perego, F. Giberti, M. Parrinello
Published in: The European Physical Journal Special Topics, Issue 225/8-9, 2016, Page(s) 1621-1628, ISSN 1951-6355
Publisher: EDP Sciences
DOI: 10.1140/epjst/e2016-60094-x

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

Author(s): Federica Moraca, Jussara Amato, Francesco Ortuso, Anna Artese, Bruno Pagano, Ettore Novellino, Stefano Alcaro, Michele Parrinello, Vittorio Limongelli
Published in: Proceedings of the National Academy of Sciences, Issue 114/11, 2017, Page(s) E2136-E2145, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1612627114

A variational approach to nucleation simulation

Author(s): Pablo M. Piaggi, Omar Valsson, Michele Parrinello
Published in: Faraday Discuss., Issue 195, 2016, Page(s) 557-568, ISSN 1359-6640
Publisher: Royal Society of Chemistry
DOI: 10.1039/C6FD00127K

Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

Author(s): Michele Invernizzi, Omar Valsson, Michele Parrinello
Published in: Proceedings of the National Academy of Sciences, Issue 114/13, 2017, Page(s) 3370-3374, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1618455114

Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation

Author(s): Aydin Ozcan, Claudio Perego, Matteo Salvalaglio, Michele Parrinello, Ozgur Yazaydin
Published in: Chem. Sci., Issue 8/5, 2017, Page(s) 3858-3865, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/C6SC04978H

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

Author(s): Pablo M. Piaggi, Omar Valsson, Michele Parrinello
Published in: Physical Review Letters, Issue 119/1, 2017, Page(s) 015701-1 - 015701-4, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.119.015701

How Collective Phenomena Impact CO 2 Reactivity and Speciation in Different Media

Author(s): Daniela Polino, Emanuele Grifoni, Roger Rousseau, Michele Parrinello, Vassiliki-Alexandra Glezakou
Published in: The Journal of Physical Chemistry A, Issue 124/20, 2020, Page(s) 3963-3975, ISSN 1089-5639
Publisher: American Chemical Society
DOI: 10.1021/acs.jpca.9b11744

Rethinking Metadynamics: From Bias Potentials to Probability Distributions

Author(s): Michele Invernizzi, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 11/7, 2020, Page(s) 2731-2736, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c00497

Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics

Author(s): Jayashrita Debnath, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 11/13, 2020, Page(s) 5076-5080, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c01125

A local fingerprint for hydrophobicity and hydrophilicity: From methane to peptides

Author(s): S. Pérez-Conesa, Pablo M. Piaggi, Michele Parrinello
Published in: The Journal of Chemical Physics, Issue 150/20, 2019, Page(s) 204103, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5088418

Tautomeric Equilibrium in Condensed Phases

Author(s): Emanuele Grifoni, GiovanniMaria Piccini, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 16/10, 2020, Page(s) 6027-6031, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00519

Data-Driven Collective Variables for Enhanced Sampling

Author(s): Luigi Bonati, Valerio Rizzi, Michele Parrinello
Published in: The Journal of Physical Chemistry Letters, Issue 11/8, 2020, Page(s) 2998-3004, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c00535

A metadynamics perspective on the reduction mechanism of the Pt(IV) asplatin prodrug

Author(s): Fortuna Ponte, GiovanniMaria Piccini, Emilia Sicilia, Michele Parrinello
Published in: Journal of Computational Chemistry, Issue 41/4, 2019, Page(s) 290-294, ISSN 0192-8651
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jcc.26100

Dimer Metadynamics

Author(s): Marco Nava, Ferruccio Palazzesi, Claudio Perego, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 13/2, 2017, Page(s) 425-430, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.6b00691

Molecular Mechanism of Gas Solubility in Liquid: Constant Chemical Potential Molecular Dynamics Simulations

Author(s): Narjes Ansari, Tarak Karmakar, Michele Parrinello
Published in: Journal of Chemical Theory and Computation, Issue 16/8, 2020, Page(s) 5279-5286, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00450

Augmented Harmonic Linear Discriminant Analysis

Author(s): Brotzakis Zacharias Faidon, Mendels Dan, Parrinello Michele
Published in: 2019
Publisher: arXiv.org

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