title: A versatile AMBER-Gaussian QM/MM interface through PUPIL.
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.
authors.affiliation: Departament d'Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça.Rei 15, 08700-Igualada, Spain.
authors.forename: Juan
authors.initials: J
authors.lastname: Torras
authors.forename: Gustavo de M
authors.initials: Gde M
authors.lastname: Seabra
authors.forename: Erik
authors.initials: E
authors.lastname: Deumens
authors.forename: S B
authors.initials: SB
authors.lastname: Trickey
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg
mesh_terms: D004151:Dipeptides / Q000737:chemistry; D008956:Models, Chemical; D009573:Nitrites / Q000737:chemistry; D011789:Quantum Theory; D012984:Software
chemical_list: D004151:Dipeptides; D009573:Nitrites; C021229:oxyhyponitrite; C002956:alanylalanine