Comment on “a minimal implementation of the AMBER–GAUSSIAN interface for Ab Initio QM/MM‐MD simulation” |
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| Authors: | Benjamin P. Roberts Gustavo M. Seabra Adrian E. Roitberg Kenneth M. Merz Erik Deumens Juan Torras Samuel B. Trickey |
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| Affiliation: | 1. Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida 32611‐8435;2. Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611‐8435;3. Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco CEP 50.740‐540, Brazil;4. Departament d'Enginyeria Química, EEI, Universitat Politècnica de Catalunya, P?a del Rei 15, Igualada 08700, Spain |
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| Abstract: | We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011 , 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN‐03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open‐source codes more generally. © 2012 Wiley Periodicals, Inc. |
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| Keywords: | multiscale simulations hybrid QM/MD or QM/MM simulations AMBER‐PUPIL‐GAUSSIAN interface |
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