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WIREs Comput Mol Sci
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ChemShell—a modular software package for QM/MM simulations

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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. This article is categorized under: Software > Quantum Chemistry Software > Molecular Modeling
Visualization (left) of aldehyde oxidoreductase. The enzymatic system is shown in ribbon style, the reaction center including the substrate is drawn as a space‐filling representation, and the additional water molecules are in a stick representation. In a QM/MM representation (right), this reduces to the QM region (shown in a space‐filling representation) surrounded by a cloud of positive and negative point charges, with the same position as the atoms in the enzyme.
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An ionic embedded cluster model of an aluminum‐doped zinc oxide surface, showing the transition state for hydrogen interchange between an adsorbed carbon dioxide and two hydrogen molecules. In the left image the cluster, cut from a bulk periodic surface, is shown together with the adsorbates. In the right image, the QM/MM representation is illustrated, with the QM region and QM/MM boundary atoms shown in a space‐filling representation surrounded by point charges. The point charges correspond to classical force field atoms (each sphere representing a core and shell) and an outer layer of external point changes fitted to reproduce the electrostatic influence of the bulk material.
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Software > Molecular Modeling
Software > Quantum Chemistry

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