(566g) Molmod: A Force Field Database for Molecular Simulations of Fluids

The MolMod force field database [1] is presented. The MolMod database is an open-access web-based database for classical force fields for fluids that can be used in molecular dynamics or Monte Carlo simulations for modeling a large variety of thermodynamic properties as well as for the simulation of nanoscopic processes. The MolMod database contains both component-specific force fields and transferable force fields. In a component-specific force field, the model parameters of a given force field are only valid for a certain component. A transferable force field, on the other hand, is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a force field model for a given component. The vast majority of force fields in the database was parametrized using vapor-liquid equilibrium data and accordingly describe such data well. In many cases, also predictions of other properties, like transport and interfacial properties, were tested and found to be in good agreement with experimental data. Many of the molecular models were also successfully tested for modeling mixtures using combination rules like those of Lorentz and Berthelot.
The MolMod database presently comprises approximately 700 component-specific force fields – and is constantly growing. This includes mostly molecular substances and also some ionic components. The database comprises both rigid force fields as well as flexible force fields with internal degrees of freedom. Moreover, the MolMod database comprises eight transferable force field that can be used for describing a large number of components. Force field developers are invited so submit their models to the MolMod admins for being included in the database.
For transferable force fields, the MolMod database contains a graphical user interface in the front-end of the website that enables the user to construct essentially any organic molecule. Moreover, the user can specify, which transferable force field is to be used, e.g. TraPPE or OPLS. Then, the website provides the actual force field parameters for the chosen molecule (cf. Fig. 1).
For implementing transferable force fields in the MolMod database, a new SQL-based data scheme was developed, which provides a machine-readable format for integrating a given transferable force field. This force field scheme is generalized such that different transferable force fields can be formulated within the data scheme. The data scheme can be applied to all-atom as well as united-atom transferable force fields. Using this data scheme, multiple popular transferable force fields are implemented in the database, e.g. the TraPPE, OPLS-AA, and Potoff force field.
The MolMod database provides a large variety of search functionalities. For all force fields, the references to the original literature are given. The force fields are presented in a consistent unit system containing the full specifications of the molecular model. Moreover, the MolMod database provides ready-to-use input files for different simulation engines, e.g. LAMMPS [2], GROMACS [3], ms2 [4], and ls1 mardyn [5] etc. Since these molecular simulation codes are based on different approaches to realize for example multipole interactions, the geometry definition, and the rigidity of molecules, on the fly conversion routines are implemented in the database kernel. This enables researchers to include the molecular models easily in their individual work flows for predicting thermodynamic properties of fluids.

References:

[1] S. Stephan et al.: Mol. Simul. 45 (2019) 806.

[2] S. Plimpton et al.: J. Comp. Phys. 117 (1995) 1.

[3] M.J. Abraham et al.: SoftwareX 1 (2015) 19.

[4] C.W. Glass et al.: Comp. Phys. Comm. 185 (2014) 3302.

[5] C. Niethammer et al.: J. Chem. Theor. Comp. 10 (2014) 4455.