Literature DB >> 18232845

Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

Alessandro Barducci1, Giovanni Bussi, Michele Parrinello.   

Abstract

We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.

Entities:  

Year:  2008        PMID: 18232845     DOI: 10.1103/PhysRevLett.100.020603

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


  432 in total

1.  Sampling protein motion and solvent effect during ligand binding.

Authors:  Vittorio Limongelli; Luciana Marinelli; Sandro Cosconati; Concettina La Motta; Stefania Sartini; Laura Mugnaini; Federico Da Settimo; Ettore Novellino; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-11       Impact factor: 11.205

2.  Using sketch-map coordinates to analyze and bias molecular dynamics simulations.

Authors:  Gareth A Tribello; Michele Ceriotti; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-16       Impact factor: 11.205

3.  Closed headpiece of integrin αIIbβ3 and its complex with an αIIbβ3-specific antagonist that does not induce opening.

Authors:  Jieqing Zhu; Jianghai Zhu; Ana Negri; Davide Provasi; Marta Filizola; Barry S Coller; Timothy A Springer
Journal:  Blood       Date:  2010-08-02       Impact factor: 22.113

4.  Linking well-tempered metadynamics simulations with experiments.

Authors:  Alessandro Barducci; Massimiliano Bonomi; Michele Parrinello
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

5.  Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics.

Authors:  Davide Provasi; Marta Filizola
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

6.  Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Authors:  Pratyush Tiwary; Jagannath Mondal; Joseph A Morrone; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

Review 7.  Constraint methods that accelerate free-energy simulations of biomolecules.

Authors:  Alberto Perez; Justin L MacCallum; Evangelos A Coutsias; Ken A Dill
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

8.  Mutant bacterial sodium channels as models for local anesthetic block of eukaryotic proteins.

Authors:  Natalie E Smith; Ben Corry
Journal:  Channels (Austin)       Date:  2016-02-06       Impact factor: 2.581

9.  Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes.

Authors:  Shashank Pant; Emad Tajkhorshid
Journal:  J Comput Chem       Date:  2019-11-25       Impact factor: 3.376

10.  Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations.

Authors:  Dalibor Trapl; Izabela Horvacanin; Vaclav Mareska; Furkan Ozcelik; Gozde Unal; Vojtech Spiwok
Journal:  Front Mol Biosci       Date:  2019-04-18
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.