Introduction

COBRAMM is a program package interfacing widely known commercial & academic software for molecular modeling (spanning from electronic structure and molecular mechanics computations). It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited state electronic structure computations within a combined quantum mechanical/molecular mechanical (QM/MM) framework to bridge the atomistic to the nano-scale.

The user can perform all necessary steps to simulate chemical reactions in complex environments (ranging from solvents to bio-polymers) and model the interaction of those systems with light to simulate their spectroscopy, as well as their photoinduced dynamics. Starting from ground state optimizations, reaction path computations, initial conditions sampling, spectroscopy simulation and photodynamics including deactivation events, COBRAMM is designed to assist the characterization and analysis of complex molecular materials and their properties as well as the interpretation of the recorded spectra ranging from steady-state to time resolved measurements. Various tools help the user to setup the system of interest and analyze the results.

COBRAMM is currently interfaced with Amber for MM calculations and Gaussian, (Open)Molcas and Molpro for QM calculations.  

Capabilities

• subtractive QM/MM scheme, with electrostatic embedding and a hydrogen link-atom approach
• up to three layers in the QM/MM method: QM atoms, movable MM atoms and frozen MM atoms
• interface to state-of-the-art QM codes for ground and excited state electronic structure with wavefunction and TD-DFT methods
• PES exploration through Gaussian optimization algorithm: minima and transition state search, photochemical MEP from the Franck-Condon geometry, conical intersection search
• normal modes analysis with computation of numerical second derivatives at any level of QM
• numerical computation of gradient and non-adiabatic couplings with the CASPT2 and the RASSCF method
• molecular dynamics in the micro-canonical ensemble at any level of QM
• non-adiabatic molecular dynamics with CASSCF and CASPT2 and different surface hopping algorithms: a simple diabatic hopping and Tully's Fewest Switches Surface Hopping (FSSH) with decoherence correction

The COBRAMM software is still under development: new features are constantly added by the different research teams.

Developers

COBRAMM was initially developed at the Department of Chemistry "G. Ciamician" of the University of Bologna by Dr. Piero Altoè and Dr. Marco Stenta, under the supervision of Dr. Marco Garavelli and Prof. Andrea Bottoni. 

Since 2019 the code has been subject to a completely object oriented rewrite started by Dr. Matteo Bonfanti and further advanced by Dr. Davide Avagliano and Dr. Flavia Aleotti.

COBRAMM is now maintained by the Computational Photophysics and Photochemistry Group of Prof. Garavelli and Prof. Nenov, at the Department of Industrial Chemistry "Toso Montanari" of the University of Bologna. Current developers include Dr. Flavia Aleotti and Dr. Davide Avagliano.

Oliver Weingart (Heinrich-Heine-University Düsseldorf) has been contributing to the development of the code since 2008.