Literature DB >> 25046020

A time-independent free energy estimator for metadynamics.

Pratyush Tiwary1, Michele Parrinello.   

Abstract

Metadynamics is a powerful and well-established enhanced sampling method for exploring and quantifying free energy surfaces of complex systems as a function of appropriately chosen variables. In the limit of long simulation time, metadynamics converges to the exact free energy surface plus a time-dependent constant. In this article, we analyze in detail this time-dependent constant. We show an easy way to calculate it, and by explicitly calculating the time dependence of this constant, we are able to derive a time-independent and locally convergent free energy estimator for metadynamics. We also derive an alternate procedure for obtaining the full unbiased distributions of generic operators from biased metadynamics simulations and explicitly test its usefulness.

Year:  2014        PMID: 25046020     DOI: 10.1021/jp504920s

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  74 in total

1.  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

2.  Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.

Authors:  Kristen A Marino; Marta Filizola
Journal:  Methods Mol Biol       Date:  2018

3.  Predicting polymorphism in molecular crystals using orientational entropy.

Authors:  Pablo M Piaggi; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-20       Impact factor: 11.205

4.  Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2016-04-07       Impact factor: 3.488

5.  How wet should be the reaction coordinate for ligand unbinding?

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2016-08-07       Impact factor: 3.488

6.  Nanomechanics of Type I Collagen.

Authors:  Sameer Varma; Joseph P R O Orgel; Jay D Schieber
Journal:  Biophys J       Date:  2016-07-12       Impact factor: 4.033

7.  Spectral gap optimization of order parameters for sampling complex molecular systems.

Authors:  Pratyush Tiwary; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-29       Impact factor: 11.205

8.  Predicting reaction coordinates in energy landscapes with diffusion anisotropy.

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2017-10-21       Impact factor: 3.488

9.  Free-Energy Landscape of the Amino-Terminal Fragment of Huntingtin in Aqueous Solution.

Authors:  Vincent Binette; Sébastien Côté; Normand Mousseau
Journal:  Biophys J       Date:  2016-03-08       Impact factor: 4.033

10.  Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.

Authors:  Changwon Yang; Mandar Kulkarni; Manho Lim; Youngshang Pak
Journal:  Nucleic Acids Res       Date:  2017-12-15       Impact factor: 16.971

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