Literature DB >> 12857293

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

Marcella Iannuzzi1, Alessandro Laio, Michele Parrinello.   

Abstract

The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metadynamics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.

Year:  2003        PMID: 12857293     DOI: 10.1103/PhysRevLett.90.238302

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  61 in total

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Journal:  Nat Mater       Date:  2010-09       Impact factor: 43.841

2.  Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels.

Authors:  Bernd Ensing; Michael L Klein
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-29       Impact factor: 11.205

3.  The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections.

Authors:  Volodymyr Babin; Christopher Roland; Thomas A Darden; Celeste Sagui
Journal:  J Chem Phys       Date:  2006-11-28       Impact factor: 3.488

4.  Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases.

Authors:  Matteo Dal Peraro; Alejandro J Vila; Paolo Carloni; Michael L Klein
Journal:  J Am Chem Soc       Date:  2007-02-17       Impact factor: 15.419

5.  Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.

Authors:  Vojtech Spiwok; Blanka Králová; Igor Tvaroska
Journal:  J Mol Model       Date:  2008-07-17       Impact factor: 1.810

6.  The Janus-faced role of external forces in mechanochemical disulfide bond cleavage.

Authors:  Przemyslaw Dopieralski; Jordi Ribas-Arino; Padmesh Anjukandi; Martin Krupicka; Janos Kiss; Dominik Marx
Journal:  Nat Chem       Date:  2013-06-16       Impact factor: 24.427

Review 7.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

8.  A spin-1 representation for dual-funnel energy landscapes.

Authors:  Justin E Elenewski; Kirill A Velizhanin; Michael Zwolak
Journal:  J Chem Phys       Date:  2018-07-21       Impact factor: 3.488

9.  Insight into the folding inhibition of the HIV-1 protease by a small peptide.

Authors:  Massimiliano Bonomi; Francesco L Gervasio; Guido Tiana; Davide Provasi; Ricardo A Broglia; Michele Parrinello
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

10.  Microscopic Mechanism of Antibiotics Translocation through a Porin.

Authors:  Matteo Ceccarelli; Christophe Danelon; Alessandro Laio; Michele Parrinello
Journal:  Biophys J       Date:  2004-07       Impact factor: 4.033

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