Literature DB >> 26575539

A comment on the reweighting method for accelerated molecular dynamics simulations.

Zhifeng Jing, Huai Sun1.   

Abstract

Accelerated molecular dynamics (aMD) is a popular method for biomolecular simulations. The estimator to recover the true free energy profile, termed "reweighting", constitutes a critical part of aMD. Recently the second order cumulant expansion has been recommended as an improved reweighting method. Here we examine the validity of this reweighting method and provide an insight into the need for selecting appropriate boost potentials.

Year:  2015        PMID: 26575539     DOI: 10.1021/acs.jctc.5b00236

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  4 in total

1.  Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD.

Authors:  Anna S Kamenik; Ursula Kahler; Julian E Fuchs; Klaus R Liedl
Journal:  J Chem Theory Comput       Date:  2016-07-11       Impact factor: 6.006

2.  Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.

Authors:  Anna S Kamenik; Uta Lessel; Julian E Fuchs; Thomas Fox; Klaus R Liedl
Journal:  J Chem Inf Model       Date:  2018-04-20       Impact factor: 4.956

3.  Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem.

Authors:  Chetna Tyagi; Tamás Marik; Csaba Vágvölgyi; László Kredics; Ferenc Ötvös
Journal:  Int J Mol Sci       Date:  2019-08-30       Impact factor: 5.923

4.  Molecular Modeling of Chemosensory Protein 3 from Spodoptera litura and Its Binding Property with Plant Defensive Metabolites.

Authors:  Sujata Singh; Chetna Tyagi; Irfan A Rather; Jamal S M Sabir; Md Imtaiyaz Hassan; Archana Singh; Indrakant Kumar Singh
Journal:  Int J Mol Sci       Date:  2020-06-06       Impact factor: 5.923

  4 in total

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