title: PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.
abstract: PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.
authors.affiliation: Department of Chemical Engineering, EEI, Universitat Politècnica de Catalunya, Igualada, Spain. Electronic address: joan.torras@upc.edu.
authors.forename: Juan
authors.initials: J
authors.lastname: Torras
authors.affiliation: Centre for eResearch, The University of Auckland, Auckland, New Zealand.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Roberts
authors.affiliation: Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco, Brazil.
authors.forename: Gustavo M
authors.initials: GM
authors.lastname: Seabra
authors.affiliation: Departments of Physics and of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida, USA. Electronic address: trickey@qtp.ufl.edu.
authors.forename: Samuel B
authors.initials: SB
authors.lastname: Trickey
mesh_terms: D005293:Ferritins / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D012984:Software; D013816:Thermodynamics
chemical_list: D009211:Myoglobin; D005293:Ferritins
keywords: Biomolecular modeling; Computational biology; Hybrid methods; Multi-scale simulation; Multiple actives zones; PUPIL; QM/MM; QM/MM-MD