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All input files can be downloaded: Files.

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For more information of this section, please refer to these pages:

• qmmm

• Density Functional Theory Calculations

• Semi-empirical Quantum Chemistry Methods

• Molecular Mechanics Calculations

QM/MM Simulations

This tutorial will lead you step by step to do standard molecular dynamics (MD) simulations using Qbics. Assume you have read Density Functional Theory Calculations, Semi-empirical Quantum Chemistry Methods, and Molecular Mechanics Calculations.

General Considerations

To perform a QM/MM simulation, typically you need to follow the following steps:

• Prepare input files that can be used for pure MM simulations. Please refer to Molecular Mechanics Calculations for details;

• Relax the system using MM method. This step is optional, but it is highly recommended to ensure the system is in a reasonable state before QM/MM calculations;

• Select a QM region, and do QM/MM calculations. The QM method can be DFT, xTB, or NDDO. Please refer to Density Functional Theory Calculations and Semi-empirical Quantum Chemistry Methods for details.

During the QM/MM simulation, there should NOT be covalent bonds forming or breaking between QM and MM region. Otherwise, the QM region shold be extended. The best case is that there is no covalent bond between QM and MM region. But, Qbics can handle specific cases, where the QM region is covalently bonded to sp³carbon atoms in the MM region.

Note that, in the QM region, any covalent bonds formation or breaking is allowed, no matter what connectivity is defined in the topology file.

In the following, we will demonstrate how to do QM/MM simulations with Qbics.

Example: in Water Box