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Implementing dimer metadynamics using gromacs.

Authors
  • Nava, M1
  • 1 Department of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900, Lugano, Switzerland. , (Switzerland)
Type
Published Article
Journal
Journal of Computational Chemistry
Publisher
Wiley (John Wiley & Sons)
Publication Date
Sep 30, 2018
Volume
39
Issue
25
Pages
2126–2132
Identifiers
DOI: 10.1002/jcc.25386
PMID: 30306568
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

We develop a Gromacs implementation of dimer metadynamics (DM) (JCTC 13, 425 [2017]) for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom nonbonded interactions. We demonstrate this implementation on alanine dipeptide in vacuum and in water, and on the 12-residue alanine polypeptide in water and compare the results with a standard multiple-replica technique such as parallel tempering. In all the considered cases, this comparison is consistent and the results with DM are smoother and require shorter simulations, thus proving the consistency and effectiveness of this Gromacs implementation. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

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