Literature DB >> 24006969

A boundary correction algorithm for metadynamics in multiple dimensions.

Michael McGovern1, Juan de Pablo.   

Abstract

Metadynamics is an efficient method for simulation of the free energy of many-particle systems. Over the last several years it has been applied to study a wide variety of systems, ranging from simple fluids to biological macromolecules. The method relies on uniform sampling along specified collective variables or order parameters. Such order parameters, however, are often bounded, and metadynamics algorithms as originally developed suffer from systematic errors at the corresponding boundaries. While several approaches have been proposed in the past to correct these errors for unidimensional systems, no method exists to fully correct these errors in multi-dimensional systems at points where multiple boundaries meet. Here we present a correction scheme that circumvents this limitation.

Year:  2013        PMID: 24006969     DOI: 10.1063/1.4818153

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


  5 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.  Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.

Authors:  Benjamin Pampel; Omar Valsson
Journal:  J Chem Theory Comput       Date:  2022-06-28       Impact factor: 6.578

3.  Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics.

Authors:  Rui Sun; Olaseni Sode; James F Dama; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2017-04-04       Impact factor: 6.006

4.  Secondary Structure of Rat and Human Amylin across Force Fields.

Authors:  Kyle Quynn Hoffmann; Michael McGovern; Chi-Cheng Chiu; Juan J de Pablo
Journal:  PLoS One       Date:  2015-07-29       Impact factor: 3.240

5.  Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction.

Authors:  James F Dama; Glen M Hocky; Rui Sun; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2015-11-20       Impact factor: 6.006

  5 in total

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