Introduction#

Welcome to the comprehensive Solvate Suite User Guide! The Solvate Suite is a modular and integrated toolkit designed to streamline the preparation and processing of molecular systems with explicit solvents, bridging molecular dynamics (MD) simulations with quantum chemistry calculations. This package was conceived to meet the needs of researchers working at the interface between classical mechanics and electronic structure methods, especially in contexts that require a more realistic modeling of solvated environments, such as reaction mechanisms in solution, spectroscopic studies, and thermochemical properties.

With a flexible and highly customizable approach, Solvate Suite allows you to:

• Create initial configurations for AIMD/BOMD simulations with ORCA or classical MD simulations with GROMACS;

• Generate solvation boxes with various solvents and force fields (OPLS-AA, GROMOS, CHARMM, and AMBER) from diverse sources (GROMACS database, LigParGen, ATB, or Q-Force);

• Integrate data from molecular dynamics simulations with input files for electronic structure calculations (semiempirical, DFT, MP2, etc.);

• Automate repetitive steps such as snapshot extraction, and input preparation for software like Gaussian, ORCA, xTB, and GROMACS;

• Perform statistical and structural analyses of solvent environments around target species.

This manual was written to guide users — from beginners to advanced — through the efficient use of Solvate Suite’s features. Throughout the chapters, you will find step-by-step instructions, practical examples, useful tips, and conceptual explanations that help you understand not only the “how”, but also the “why” of each step.

Get ready to accelerate your computational workflow and explore complex systems with greater control, reproducibility, and speed.