Installation Instructions

Simulation Box Creation

- PackMol v20.14.2 (Initial configurations for Molecular Dynamics)
- Q-Force v1.0 (Quantum Mechanically Augmented Molecular Force Fields)

Electronic Structure and Molecular Dynamics Simulation Programs

- xTB v6.6.1 (Semiempirical Extended Tight-Binding Program Package)
- CREST v2.12 (Conformer-Rotamer Ensemble Sampling Tool)
- ORCA 5.0 (General-Purpose Quantum Chemistry Package)
- GROMACS 2023.3 (Package to Perform Molecular Dynamics)

Visualization Programs

- JMol (Java Viewer for Chemical Structures)
- VMD (Visual Molecular Dynamics)

Scripts Interpreter and Libraries

- Zip & UnZip (Compressing and decompressing files)
- Python 3.10 (Python Programming Language)
- MatPlotLib 3.5 (Library for Creating Visualizations in Python)
- Tqdm 4.65 (Library for Creating Progress Bars)
- PyQt5 5.15 (Python Programming Language and the Qt Library)

The suite is distributed pre-compiled for Linux systems, being only necessary to configure it. To do this:

❶ Download manually the latest release or beta version, or run one of the commands below in your terminal:

wget https://github.com/otaviolsantana/solvate/archive/refs/heads/main.zip

wget https://github.com/otaviolsantana/solvate-beta/archive/refs/heads/main.zip

❷ Unzip the “main.zip” file with your preferred zip manager or use the command:

unzip main.zip

Note: a directory named solvate-main will be extracted. Inside this directory, you will find all the binaries and configuration files for Solvate Suite. Since this is a precompiled version, you will only need to adjust a few settings to ensure the suite functions correctly. If you prefer, rename the directory to solvate and move it to your desired installation location.

❸ Using your preferred text editor, open the “solvate.config” file and add the paths to the directories containing the programs you want Solvate Suite to manage. In your script, locate the section below and fill it in with the paths to the directories of your programs.

INI_SVT=/opt/solvate
DIR_GSN=/opt/gsn #Gaussian
DIR_GVW=/opt/gvw #GaussView
DIR_ORC=/opt/orca #ORCA
DIR_XTB=/opt/xtb #xTB
DIR_GMX=/opt/gmx #GROMACS
DIR_VMD=/opt/vmd #VMD
DIR_MPI=/opt/openmpi #OpenMPI
DIR_PCK=/opt/packmol #PackMol
DIR_QFC=/opt/qforce #QForce

Note #1: replace “/opt/solvate” with the path you set for the suite directory.
Note #2: you should specify the path to the installation directory of the programs, not directly to the executables.

❹ In the “solvate.profile” file, you need to modify the line:

export HOME_SOLVATE=“Solvate Suite Directory”

For example, if Solvate Suite is installed in “/opt/solvate”, you should change the line to:

export HOME_SOLVATE=/opt/solvate

Note: this section is found in the first lines of the “solvate.profile” file.

❺ Make the “solvate.config” script file executable with the following command:

chmod +x solvate.config

and run the script with:

./solvate.config

Finally, add the following lines to your bash file, located at /home/$USER/.bashrc:

# Solvate Suite
export HOME_SOLVATE=“Solvate Suite Directory”
source $HOME_SOLVATE/solvate.profile

Note: the path to be added should be the same as the one you specified in step 4, under HOME_SOLVATE.