title: GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.
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.
authors.affiliation: Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos–SP, Brazil. ferbachega@gmail.com
authors.forename: José Fernando R
authors.initials: JF
authors.lastname: Bachega
authors.forename: Luís Fernando S M
authors.initials: LF
authors.lastname: Timmers
authors.forename: Lucas
authors.initials: L
authors.lastname: Assirati
authors.forename: Leonardo R
authors.initials: LR
authors.lastname: Bachega
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Field
authors.forename: Troy
authors.initials: T
authors.lastname: Wymore
mesh_terms: D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012984:Software / Q000592:standards