Literature DB >> 26696048

μ-tempered metadynamics: Artifact independent convergence times for wide hills.

Bradley M Dickson1.   

Abstract

Recent analysis of well-tempered metadynamics (WTmetaD) showed that it converges without mollification artifacts in the bias potential. Here, we explore how metadynamics heals mollification artifacts, how healing impacts convergence time, and whether alternative temperings may be used to improve efficiency. We introduce "μ-tempered" metadynamics as a simple tempering scheme, inspired by a related mollified adaptive biasing potential, that results in artifact independent convergence of the free energy estimate. We use a toy model to examine the role of artifacts in WTmetaD and solvated alanine dipeptide to compare the well-tempered and μ-tempered frameworks demonstrating fast convergence for hill widths as large as 60(∘) for μTmetaD.

Entities:  

Year:  2015        PMID: 26696048     DOI: 10.1063/1.4937939

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  3 in total

1.  A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.

Authors:  Bradley M Dickson; Parker W de Waal; Zachary H Ramjan; H Eric Xu; Scott B Rothbart
Journal:  J Chem Phys       Date:  2016-10-21       Impact factor: 3.488

2.  The structural basis of the dominant negative phenotype of the Gαi1β1γ2 G203A/A326S heterotrimer.

Authors:  Ping Liu; Ming-Zhu Jia; X Edward Zhou; Parker W De Waal; Bradley M Dickson; Bo Liu; Li Hou; Yan-Ting Yin; Yan-Yong Kang; Yi Shi; Karsten Melcher; H Eric Xu; Yi Jiang
Journal:  Acta Pharmacol Sin       Date:  2016-08-08       Impact factor: 6.150

Review 3.  Computational methods for exploring protein conformations.

Authors:  Jane R Allison
Journal:  Biochem Soc Trans       Date:  2020-08-28       Impact factor: 5.407

  3 in total

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