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GTKDynamo: A PyMOL plug‐in for QC/MM hybrid potential simulations
Author(s) -
Bachega José Fernando R.,
Timmers Luís Fernando S. M.,
Assirati Lucas,
Bachega Leonardo R.,
Field Martin J.,
Wymore Troy
Publication year - 2013
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23346
Subject(s) - computer science , plug in , visualization , process (computing) , quantum chemical , computational science , molecular dynamics , chemistry , computational chemistry , molecule , programming language , data mining , organic chemistry
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. © 2013 Wiley Periodicals, Inc.