The modeling and study of liquid systems are essential for understanding a broad spectrum of chemical and biological processes. Solutions and solvents play fundamental roles in chemical reactions, biomolecular interactions, and material behavior. To address these complex dynamics, we introduce the Solvate Suite, a comprehensive, modular command-line interface designed specifically for molecular simulations of liquid systems and microsolvation modeling.
The Solvate Suite specializes in analyzing solute-solvent interactions and the behavior of liquids under various simulated conditions. Seamlessly integrating with computational chemistry tools such as ORCA, xTB, GROMACS, PackMol, Q-Force, and others, it streamlines computational experiments involving liquid systems by automating the creation of simulation boxes and topologies with customizable parameters.
Additionally, the Solvate Suite offers advanced graphical and statistical analysis features and tools to extract trajectory configurations using multiple filters. One of its standout features is a multiscale approach to microsolvation modeling, which utilizes equilibrated dynamics to identify favorable solute-solvent interactions. This enables precise optimization of clusters and accurate free energy calculations, free from the contamination of imaginary frequencies. The suite is a powerful tool for exploring and modeling liquid systems, driving meaningful advances in chemistry, biology, and materials science.
The Solvate Suite is a comprehensive software package designed to address various challenges in molecular modeling. The suite's modules interface with widely used open-source software, facilitating the sequential treatment of all stages of molecular modeling involving explicit interaction of the species of interest with the solvent, employing both molecular simulation procedures and electronic structure calculations in a hybrid approach (explicit/implicit solvation). Their structure comprises multiple modules, each dedicated to addressing key aspects of molecular modeling:
(1) Creation of Simulation Box: The module PACKS allows users to create the simulation box according to specified criteria, including the number of solvent molecules, shape and density of the box, solute/solvent concentration, or proportions between solvent mixtures. It also determines force field parameters and constructs the system's topology for classical dynamics-based simulation methods.
(2) Submission of Simulations: From the module MDRUN, the user can run simulations with a minimum set of adjusted parameters. These parameters can be modified during runtime or users can use their own simulation parameters.
(3) Analysis of Simulated Properties: The module DATAS analyzes various simulated properties such as pressure, temperature, density, short-range interaction, total potential energy, and radial distribution function. It includes statistical analysis, graphical representation, and property extraction based on different criteria like block analysis and pressure filter.
(4) Treatment of Microsolvation Clusters: Users can select a predefined number of hydrogen-bonded structures or microsolvation clusters with MICRO module, along with the corresponding solvent molecules per cluster, identified from the simulation trajectory file based on solute-solvent proximity. The subsequent modules conduct semi-empirical quantum chemistry calculations to choose microsolvation clusters for the calculation of mean free energy. These modules offer various treatment options, including fixed geometries from the simulation, fully optimized cluster structures, or a relaxed solvent cavity with optimized solute geometry. The procedure eliminates imaginary frequencies, applies quasi-harmonic corrections, and utilizes extrapolation methods for free energy calculations at a user-specified level of theory.
(5) Management of Generated Files: The suite manages the significant number of files generated throughout the modeling process, ensuring efficient organization and storage.
Overall, the Solvate Suite provides a comprehensive solution for molecular modeling tasks, addressing various complexities encountered in explicit solvent simulations.
If you use Solvate Suite, please cite:
Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling
Otávio L. Santana, Daniel G. Silva, Sidney R. Santana
J. Chem. Inf. Model. 2024, 64, 9, 3767–3778
SOLVATE is a free software: you can redistribute it under the terms of the BSD 3-Clause License. This software is provided by the copyright holders and contributors “as is”, and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose, are disclaimed. In no event shall the copyright holder or contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.
