Literature DB >> 26787868

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.

Patrick Shaffer1, Omar Valsson2, Michele Parrinello3.   

Abstract

The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.

Entities:  

Keywords:  biomolecular simulation; enhanced sampling; free-energy calculation; protein folding

Mesh:

Substances:

Year:  2016        PMID: 26787868      PMCID: PMC4747745          DOI: 10.1073/pnas.1519712113

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  39 in total

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

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Journal:  Phys Rev Lett       Date:  2008-01-18       Impact factor: 9.161

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7.  Locating landmarks on high-dimensional free energy surfaces.

Authors:  Ming Chen; Tang-Qing Yu; Mark E Tuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-03       Impact factor: 11.205

8.  From metadynamics to dynamics.

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Journal:  Phys Rev Lett       Date:  2013-12-03       Impact factor: 9.161

9.  Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering.

Authors:  Tong Zhang; Phuong H Nguyen; Jessica Nasica-Labouze; Yuguang Mu; Philippe Derreumaux
Journal:  J Phys Chem B       Date:  2015-05-29       Impact factor: 2.991

10.  Gaussian-mixture umbrella sampling.

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  6 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-15       Impact factor: 11.205

2.  Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

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Journal:  Phys Biol       Date:  2018-03-09       Impact factor: 2.583

4.  Deep learning the slow modes for rare events sampling.

Authors:  Luigi Bonati; GiovanniMaria Piccini; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-02       Impact factor: 11.205

5.  Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.

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Journal:  J Chem Theory Comput       Date:  2016-05-16       Impact factor: 6.006

6.  Local and global perspectives on diffusion maps in the analysis of molecular systems.

Authors:  Z Trstanova; B Leimkuhler; T Lelièvre
Journal:  Proc Math Phys Eng Sci       Date:  2020-01-15       Impact factor: 2.704

  6 in total

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