SolventSafari for GROMACS

A collection of DFT-MM/MD parametrized boxes of solvents for GROMACS.

Contents

Each solvent folder contains:

• The OPLS-AA-based force field topology, parametrized with Q-Force at the PBEPBE/6-31+G(d) level of theory
• The GROMACS-processed $SOLVENT_solventbox.gro file of the final simulation box (containing 9000 atoms
• The molecular dynamics parameter files .mdp used for energy minimizations, equilibrations, and the production run
• A workflow.sh script that automates the full simulation pipeline and reproduces the reported solvent box
• A text file containing thermodynamic data extracted using the gmx energy module (potential energy, kinetic energy, volume, temperature, pressure, and density), together with the corresponding plots

List of solvents

• Ac - Acetone - CH3COCH3
• ACN - Acetonitrile - CH3CN
• C2Cl4 - Tetrachloroethylene - C2Cl4
• CCl4 - Tetrachloromethane - CCl4
• CHCl3 - Chloroform - ChCl3
• cHex - Ciclohexane - C6H12
• ClPh - Chlorobenzene - C6H5Cl
• CS2 - Carbon Disulfide - CS2
• DCM - Dichloromethane - CH2Cl2
• DMSO - Dimethyl sulfoxide - (CH3)2SO
• EtOH - Ethane - C2H5OH
• MeOH - Methane - CH3OH
• nHex - Hexane - C6H14
• Ph - Benzene - C6H6
• THF - Tetrahydrofuran - C4H8O
• Tol - Toluene - C6H6CH3

Usage

The solvent boxes can be either installed in the top level directory of the GROMACS installation folder or used locally.

Installation (global)

1. Copy the .gro structure file into the top-level GROMACS force field directory (e.g., /opt/gromacs-2022.4/share/gromacs/top).
2. Remove all but the [moleculetype] section from the solvent .itp file and move it to the OPLS-AA force field folder (e.g., /opt/gromacs-2022.4/share/gromacs/top/oplsaa.ff/).
3. Edit watermodels.dat (located in the force field's directory, e.g., /opt/gromacs-2022.4/share/gromacs/top/oplsaa.ff/watermodels.dat), adding a new line with: <filename> (omit the file extention), <shortdescription>, and <longdescription>.

You can now use the new solvent with the -cs <solvent> flag in gmx solvate.

For further details refer to this guide.

Local use

1. Place the .gro and .itp files in your working directory.
2. Copy the [atomtypes] sections from all the .itp files (solute and solvent) at the top of the .top file. Then, comment them out it in the .itp files.
3. In the .top file, add

   #include "your_solvent.itp"
   #include "your_solute.itp"
   

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss proposed modifications.