User guide

This user guide is divided into the following sections:

• Defining molecular systems: how to define the molecular systems on which the calculations are performed, based on the available options provided by the spycci.systems submodule.

• Setting up calculations: how to set up the available spycci.engines for running your calculations. This involves deciding the program you want to use, the level of theory, and the simulation parameters.

• Running calculations: how to run different types of calculations (single point energies, geometry optimisations, molecular dynamics, etc.) using the built-in methods available in the various engines.

• Calculating properties: how to use the output of your calculations to obtain physical observables such as pKa or redox potentials

• Useful tools: a collection of useful tools for advanced users