A versatile AMBER-Gaussian QM/MM interface through PUPIL

Authors

  • Juan Torras,

    Corresponding author
    1. Departament d'Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça.Rei 15, 08700-Igualada, Spain
    • Departament d'Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça. Rei 15, 08700-Igualada, Spain
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  • Gustavo de M. Seabra,

    1. Quantum Theory Project, Departments of Physics and of Chemistry, University of Florida, Gainesville, Florida 32611-8435
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  • Erik Deumens,

    1. Quantum Theory Project, Departments of Physics and of Chemistry, University of Florida, Gainesville, Florida 32611-8435
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  • S. B. Trickey,

    1. Quantum Theory Project, Departments of Physics and of Chemistry, University of Florida, Gainesville, Florida 32611-8435
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  • Adrian E. Roitberg

    Corresponding author
    1. Quantum Theory Project, Departments of Physics and of Chemistry, University of Florida, Gainesville, Florida 32611-8435
    • Quantum Theory Project, Departments of Physics and of Chemistry, University of Florida, Gainesville, Florida 32611-8435
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Abstract

The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chemistry programs: AMBER (molecular dynamics) and Gaussian (quantum chemistry). The benefit is to allow the application of the advanced MD techniques available in AMBER to a hybrid QM/MM system in which the forces and energy on the QM part can be computed by any of the methods available in Gaussian. To illustrate, we present two example applications: A MD calculation of alanine dipeptide in explicit water, and a use of the steered MD capabilities in AMBER to calculate the free energy of reaction for the dissociation of Angeli's salt. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008

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