GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

José Fernando R Bachega; Luís Fernando S M Timmers; Lucas Assirati; Leonardo R Bachega; Martin J Field; Troy Wymore

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

José Fernando R Bachega Luís Fernando S M Timmers Lucas Assirati Leonardo R Bachega Martin J Field ¹ Troy Wymore

1 IBS - UMR 5075 - Institut de biologie structurale

Abstract : Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations.

Type de document :

Article dans une revue

Journal of Computational Chemistry, Wiley, 2013, 34 (25), pp.2190-6

Domaine :

Sciences du Vivant [q-bio] / Biochimie, Biologie Moléculaire / Biologie structurale [q-bio.BM]

Liste complète des métadonnées

http://hal.univ-grenoble-alpes.fr/hal-01662493
Contributeur : Frank Thomas <>
Soumis le : mercredi 13 décembre 2017 - 11:04:35
Dernière modification le : lundi 11 février 2019 - 16:51:21

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

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GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

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