ChemShell-a modular software package for QM/MM simulations

ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/MM coupling schemes and supporting functions for system setup, geometry optimization, and transition-state location (including those from the open-source DL-FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X-ray based quantum refinement of crystal structures, free energy methods, and excited-state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message-passing capabilities of the interfaced packages and task-farming for applications in which a number of individual QM, MM, or QM/MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications. (C) 2013 John Wiley & Sons, Ltd.