title: Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation".
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.
authors.affiliation: Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida 32611-8435, USA.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Roberts
authors.forename: Gustavo M
authors.initials: GM
authors.lastname: Seabra
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
authors.forename: Erik
authors.initials: E
authors.lastname: Deumens
authors.forename: Juan
authors.initials: J
authors.lastname: Torras
authors.forename: Samuel B
authors.initials: SB
authors.lastname: Trickey
mesh_terms: D056004:Molecular Dynamics Simulation; D011789:Quantum Theory