Variational Metadynamics

Informacje na temat projektu

VARMET

Identyfikator umowy o grant: 670227

DOI

10.3030/670227

Projekt został zamknięty

Data podpisania przez KE 29 Lipca 2015

Data rozpoczęcia 1 Stycznia 2016

Data zakończenia 31 Grudnia 2020

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity

€ 2 488 827,00

Wkład UE

€ 2 488 827,00

Koordynowany przez

UNIVERSITA DELLA SVIZZERA ITALIANA
Switzerland

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Peer reviewed articles (60)

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

Autorzy: Riccardo Capelli, Anna Bochicchio, GiovanniMaria Piccini, Rodrigo Casasnovas, Paolo Carloni, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/5, 2019, Strona(/y) 3354-3361, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.9b00118

The role of water in host-guest interaction

Autorzy: Valerio Rizzi, Luigi Bonati, Narjes Ansari, Michele Parrinello
Opublikowane w: Nature Communications, Numer 12/1, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-20310-0

Accurate Quantum Chemical Free Energies at Affordable Cost

Autorzy: GiovanniMaria Piccini, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 10/13, 2019, Strona(/y) 3727-3731, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.9b01301

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

Autorzy: Barak Hirshberg, Michele Invernizzi, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 152/17, 2020, Strona(/y) 171102, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/5.0008720

Collective variables for the study of crystallisation

Autorzy: Tarak Karmakar, Michele Invernizzi, Valerio Rizzi, Michele Parrinello
Opublikowane w: Molecular Physics, 2021, Strona(/y) e1893848, ISSN 0026-8976
Wydawca: Taylor & Francis
DOI: 10.1080/00268976.2021.1893848

Ab initio phase diagram and nucleation of gallium

Autorzy: Haiyang Niu, Luigi Bonati, Pablo M. Piaggi, Michele Parrinello
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-16372-9

Metadynamics of Paths

Autorzy: Davide Mandelli, Barak Hirshberg, Michele Parrinello
Opublikowane w: Physical Review Letters, Numer 125/2, 2020, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/physrevlett.125.026001

Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables

Autorzy: Z. Faidon Brotzakis, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/2, 2018, Strona(/y) 1393-1398, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b00827

Calculation of phase diagrams in the multithermal-multibaric ensemble

Autorzy: Pablo M. Piaggi, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 150/24, 2019, Strona(/y) 244119, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5102104

Improving collective variables: The case of crystallization

Autorzy: Yue-Yu Zhang, Haiyang Niu, GiovanniMaria Piccini, Dan Mendels, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 150/9, 2019, Strona(/y) 094509, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5081040

Unified Approach to Enhanced Sampling

Autorzy: Michele Invernizzi, Pablo M. Piaggi, Michele Parrinello
Opublikowane w: Physical Review X, Numer 10/4, 2020, ISSN 2160-3308
Wydawca: 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

Autorzy: Matteo Salvalaglio, Pratyush Tiwary, Giovanni Maria Maggioni, Marco Mazzotti, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 145/21, 2016, Strona(/y) 211925, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.4966265

Entropy based fingerprint for local crystalline order

Autorzy: Pablo M. Piaggi, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 147/11, 2017, Strona(/y) 114112, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.4998408

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

Autorzy: Rodrigo Casasnovas, Vittorio Limongelli, Pratyush Tiwary, Paolo Carloni, Michele Parrinello
Opublikowane w: Journal of the American Chemical Society, Numer 139/13, 2017, Strona(/y) 4780-4788, ISSN 0002-7863
Wydawca: American Chemical Society
DOI: 10.1021/jacs.6b12950

Collective Variables from Local Fluctuations

Autorzy: Dan Mendels, GiovanniMaria Piccini, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 9/11, 2018, Strona(/y) 2776-2781, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.8b00733

Molecular dynamics simulations of liquid silica crystallization

Autorzy: Haiyang Niu, Pablo M. Piaggi, Michele Invernizzi, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 115/21, 2018, Strona(/y) 5348-5352, ISSN 0027-8424
Wydawca: 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

Autorzy: Vinita Jagannath, Zacharias Faidon Brotzakis, Michele Parrinello, Susanne Walitza, Edna Grünblatt
Opublikowane w: Frontiers in Molecular Neuroscience, Numer 10, 2017, ISSN 1662-5099
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fnmol.2017.00342

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

Autorzy: Yi Isaac Yang, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 14/6, 2018, Strona(/y) 2889-2894, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b00231

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

Autorzy: James McCarty, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 147/20, 2017, Strona(/y) 204109, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.4998598

Chemical potential calculations in non-homogeneous liquids

Autorzy: Claudio Perego, Omar Valsson, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 149/7, 2018, Strona(/y) 072305, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5024631

Conformational Entropy as Collective Variable for Proteins

Autorzy: Ferruccio Palazzesi, Omar Valsson, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 8/19, 2017, Strona(/y) 4752-4756, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.7b01770

Frequency adaptive metadynamics for the calculation of rare-event kinetics

Autorzy: Yong Wang, Omar Valsson, Pratyush Tiwary, Michele Parrinello, Kresten Lindorff-Larsen
Opublikowane w: The Journal of Chemical Physics, Numer 149/7, 2018, Strona(/y) 072309, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5024679

Quantum Symmetry from Enhanced Sampling Methods

Autorzy: J. Runeson, M. Nava, M. Parrinello
Opublikowane w: Physical Review Letters, Numer 121/14, 2018, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/PhysRevLett.121.140602

Predicting polymorphism in molecular crystals using orientational entropy

Autorzy: Pablo M. Piaggi, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 115/41, 2018, Strona(/y) 10251-10256, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1811056115

Combining Metadynamics and Integrated Tempering Sampling

Autorzy: Yi Isaac Yang, Haiyang Niu, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 9/22, 2018, Strona(/y) 6426-6430, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.8b03005

Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics

Autorzy: Luigi Bonati, Michele Parrinello
Opublikowane w: Physical Review Letters, Numer 121/26, 2018, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/PhysRevLett.121.265701

Folding a small protein using harmonic linear discriminant analysis

Autorzy: Dan Mendels, Giovannimaria Piccini, Z. Faidon Brotzakis, Yi I. Yang, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 149/19, 2018, Strona(/y) 194113, ISSN 0021-9606
Wydawca: 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

Autorzy: Z. Faidon Brotzakis, Vittorio Limongelli, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/1, 2018, Strona(/y) 743-750, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b00934

Prion protein β 2– α 2 loop conformational landscape

Autorzy: Enrico Caldarulo, Alessandro Barducci, Kurt Wüthrich, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 114/36, 2017, Strona(/y) 9617-9622, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1712155114

Neural networks-based variationally enhanced sampling

Autorzy: Luigi Bonati, Yue-Yu Zhang, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 116/36, 2019, Strona(/y) 17641-17647, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1907975116

Enhanced Sampling of Transition States

Autorzy: Jayashrita Debnath, Michele Invernizzi, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/4, 2019, Strona(/y) 2454-2459, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b01283

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

Autorzy: Tarak Karmakar, Pablo M. Piaggi, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/12, 2019, Strona(/y) 6923-6930, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.9b00795

Identifying Slow Molecular Motions in Complex Chemical Reactions

Autorzy: GiovanniMaria Piccini, Daniela Polino, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 8/17, 2017, Strona(/y) 4197-4200, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.7b01889

Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis

Autorzy: Valerio Rizzi, Dan Mendels, Emilia Sicilia, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/8, 2019, Strona(/y) 4507-4515, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.9b00358

Path integral molecular dynamics for bosons

Autorzy: Barak Hirshberg, Valerio Rizzi, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 116/43, 2019, Strona(/y) 21445-21449, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1913365116

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

Autorzy: Valerio Rizzi, Daniela Polino, Emilia Sicilia, Nino Russo, Michele Parrinello
Opublikowane w: Angewandte Chemie International Edition, Numer 58/12, 2019, Strona(/y) 3976-3980, ISSN 1433-7851
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201900134

Metadynamics with Discriminants: A Tool for Understanding Chemistry

Autorzy: GiovanniMaria Piccini, Dan Mendels, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 14/10, 2018, Strona(/y) 5040-5044, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b00634

Microscopic description of acid–base equilibrium

Autorzy: Emanuele Grifoni, GiovanniMaria Piccini, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 116/10, 2019, Strona(/y) 4054-4057, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1819771116

A Cannibalistic Approach to Grand Canonical Crystal Growth

Autorzy: Tarak Karmakar, Pablo M. Piaggi, Claudio Perego, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 14/5, 2018, Strona(/y) 2678-2683, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b00191

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

Autorzy: Michele Invernizzi, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/4, 2019, Strona(/y) 2187-2194, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.9b00032

Temperature Dependence of Homogeneous Nucleation in Ice

Autorzy: Haiyang Niu, Yi Isaac Yang, Michele Parrinello
Opublikowane w: Physical Review Letters, Numer 122/24, 2019, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/PhysRevLett.122.245501

Searching for Entropically Stabilized Phases: The Case of Silver Iodide

Autorzy: Dan Mendels, James McCarty, Pablo M. Piaggi, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry C, Numer 122/3, 2018, Strona(/y) 1786-1790, ISSN 1932-7447
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpcc.7b11002

Multithermal-Multibaric Molecular Simulations from a Variational Principle

Autorzy: Pablo M. Piaggi, Michele Parrinello
Opublikowane w: Physical Review Letters, Numer 122/5, 2019, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/PhysRevLett.122.050601

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

Autorzy: Ferruccio Palazzesi, Matteo Salvalaglio, Alessandro Barducci, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 145, 2016, Strona(/y) 121101, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.4963340

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling

Autorzy: Patrick Shaffer, Omar Valsson, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 12/12, 2016, Strona(/y) 5751-5757, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.6b00786

Chemical potential calculations in dense liquids using metadynamics

Autorzy: C. Perego, F. Giberti, M. Parrinello
Opublikowane w: The European Physical Journal Special Topics, Numer 225/8-9, 2016, Strona(/y) 1621-1628, ISSN 1951-6355
Wydawca: EDP Sciences
DOI: 10.1140/epjst/e2016-60094-x

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

Autorzy: Federica Moraca, Jussara Amato, Francesco Ortuso, Anna Artese, Bruno Pagano, Ettore Novellino, Stefano Alcaro, Michele Parrinello, Vittorio Limongelli
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 114/11, 2017, Strona(/y) E2136-E2145, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1612627114

A variational approach to nucleation simulation

Autorzy: Pablo M. Piaggi, Omar Valsson, Michele Parrinello
Opublikowane w: Faraday Discuss., Numer 195, 2016, Strona(/y) 557-568, ISSN 1359-6640
Wydawca: Royal Society of Chemistry
DOI: 10.1039/C6FD00127K

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

Autorzy: Michele Invernizzi, Omar Valsson, Michele Parrinello
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 114/13, 2017, Strona(/y) 3370-3374, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1618455114

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

Autorzy: Aydin Ozcan, Claudio Perego, Matteo Salvalaglio, Michele Parrinello, Ozgur Yazaydin
Opublikowane w: Chem. Sci., Numer 8/5, 2017, Strona(/y) 3858-3865, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/C6SC04978H

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

Autorzy: Pablo M. Piaggi, Omar Valsson, Michele Parrinello
Opublikowane w: Physical Review Letters, Numer 119/1, 2017, Strona(/y) 015701-1 - 015701-4, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/PhysRevLett.119.015701

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

Autorzy: Daniela Polino, Emanuele Grifoni, Roger Rousseau, Michele Parrinello, Vassiliki-Alexandra Glezakou
Opublikowane w: The Journal of Physical Chemistry A, Numer 124/20, 2020, Strona(/y) 3963-3975, ISSN 1089-5639
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpca.9b11744

Rethinking Metadynamics: From Bias Potentials to Probability Distributions

Autorzy: Michele Invernizzi, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 11/7, 2020, Strona(/y) 2731-2736, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.0c00497

Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics

Autorzy: Jayashrita Debnath, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 11/13, 2020, Strona(/y) 5076-5080, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.0c01125

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

Autorzy: S. Pérez-Conesa, Pablo M. Piaggi, Michele Parrinello
Opublikowane w: The Journal of Chemical Physics, Numer 150/20, 2019, Strona(/y) 204103, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5088418

Tautomeric Equilibrium in Condensed Phases

Autorzy: Emanuele Grifoni, GiovanniMaria Piccini, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 16/10, 2020, Strona(/y) 6027-6031, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.0c00519

Data-Driven Collective Variables for Enhanced Sampling

Autorzy: Luigi Bonati, Valerio Rizzi, Michele Parrinello
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 11/8, 2020, Strona(/y) 2998-3004, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.0c00535

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

Autorzy: Fortuna Ponte, GiovanniMaria Piccini, Emilia Sicilia, Michele Parrinello
Opublikowane w: Journal of Computational Chemistry, Numer 41/4, 2019, Strona(/y) 290-294, ISSN 0192-8651
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/jcc.26100

Dimer Metadynamics

Autorzy: Marco Nava, Ferruccio Palazzesi, Claudio Perego, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 13/2, 2017, Strona(/y) 425-430, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.6b00691

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

Autorzy: Narjes Ansari, Tarak Karmakar, Michele Parrinello
Opublikowane w: Journal of Chemical Theory and Computation, Numer 16/8, 2020, Strona(/y) 5279-5286, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.0c00450

Other (1)

Augmented Harmonic Linear Discriminant Analysis

Autorzy: Brotzakis Zacharias Faidon, Mendels Dan, Parrinello Michele
Opublikowane w: 2019
Wydawca: arXiv.org