Literature DB >> 24996077

Well-tempered metadynamics converges asymptotically.

James F Dama1, Michele Parrinello2, Gregory A Voth1.   

Abstract

Metadynamics is a versatile and capable enhanced sampling method for the computational study of soft matter materials and biomolecular systems. However, over a decade of application and several attempts to give this adaptive umbrella sampling method a firm theoretical grounding prove that a rigorous convergence analysis is elusive. This Letter describes such an analysis, demonstrating that well-tempered metadynamics converges to the final state it was designed to reach and, therefore, that the simple formulas currently used to interpret the final converged state of tempered metadynamics are correct and exact. The results do not rely on any assumption that the collective variable dynamics are effectively Brownian or any idealizations of the hill deposition function; instead, they suggest new, more permissive criteria for the method to be well behaved. The results apply to tempered metadynamics with or without adaptive Gaussians or boundary corrections and whether the bias is stored approximately on a grid or exactly.

Mesh:

Year:  2014        PMID: 24996077     DOI: 10.1103/PhysRevLett.112.240602

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


  46 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.  Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations.

Authors:  Fikret Aydin; Rui Sun; Jessica M J Swanson
Journal:  Biophys J       Date:  2019-05-21       Impact factor: 4.033

3.  Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions.

Authors:  Fabrizio Marinelli; José D Faraldo-Gómez
Journal:  Biophys J       Date:  2015-06-16       Impact factor: 4.033

4.  Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants.

Authors:  Rui Sun; Yining Han; Jessica M J Swanson; Jeffrey S Tan; John P Rose; Gregory A Voth
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

5.  Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.

Authors:  Richa Singh; Rohit Bansal; Anurag Singh Rathore; Gaurav Goel
Journal:  Biophys J       Date:  2017-04-25       Impact factor: 4.033

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.  Ligand binding free-energy calculations with funnel metadynamics.

Authors:  Stefano Raniolo; Vittorio Limongelli
Journal:  Nat Protoc       Date:  2020-08-19       Impact factor: 13.491

8.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

9.  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

Review 10.  Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.

Authors:  D Wu; M I Fajer; L Cao; X Cheng; W Yang
Journal:  Methods Enzymol       Date:  2016-06-23       Impact factor: 1.600

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.