PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems

• Published in: Advances in protein chemistry and structural biology Vol. 100; p. 1
• Main Authors: Torras, Juan, Roberts, Benjamin P, Seabra, Gustavo M, Trickey, Samuel B
• Format: Journal Article Publication
• Language: English
• Published: Netherlands 01.01.2015
• Subjects: Biologia computacional; Computational biology; Ferritins - chemistry; Física; Física molecular; Humans; Molecular Dynamics Simulation; Myoglobin - chemistry; Protein Structure, Secondary; Protein Structure, Tertiary; PUPIL; Quantum Theory; Software; Thermodynamics; Àrees temàtiques de la UPC; Multiple actives zones; PUPIL; Hybrid methods; QM/MM-MD; QM/MM; Biomolecular modeling; Multi-scale simulation; Computational biology
• ISSN: 1876-1623
• DOI: 10.1016/bs.apcsb.2015.06.002

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.