Force Field generator

Force Field

The software generates the Force Field following the classic AMBER/OPLS approach. The target properties for the model calibration are the densities and heats of evaporation of liquids. The radii of the atoms, the depth of the Lennard-Jones potential, and the electrostatic potential are selected in a way to best reproduce these properties.

The classical OPLS force field well describes the thermodynamic properties of liquids. To make the process automatic and even closer reproduce the experimental values, some changes and additions were introduced into the classical approach.

Electrostatic interactions

Electrostatics is described with the help of point charges, in the simplest case, located in the centers of atoms. The charges are determined by fitting the electrostatic field created by them around the molecule to the quantum-chemical data (AMBER approach). Unlike most AMBER versions, we use COSMO PBE0/def2-svpd instead of HF/6-31*G. In the COSMO technique, a dielectric environment with the permeability corresponding to the experiment was used. If the experimental dielectric constant is not known, it was estimated iteratively from the preliminary model. For this purpose, a model was generated using some reasonable value (often 4) and a constant was estimated by the MD method. The process was repeated 2-3 times.

Thus, different models are generated for the same substance depending on the environment. To calibrate the technique, dielectric constants of pure solvents were used. When working with aqueous solutions, the water dielectric constant of 80 is recommended. Therefore, when developing biomolecular models, there is no need to change the constant.

Lennard-Jones parameters

In the proposed technique, the van der Waals interactions depend not only on the element but also on the chemical environment of the atom. The atomic volumes were estimated using the DDEC6 technique based on the PBE0/6-311+G(2d,p) calculations.

Valence interactions

We adopted a simple valence scheme with equilibrium values of bond lengths and valence angles taken from the geometry of the molecule. For accurate modeling, additional manual optimization may be required. In particular, this applies to the angular and torsion parameters. (No additional optimization was performed in the calculations for calibrating the Lennard-Jones parameters).

Distortion energy of the wave function at the transition from vacuum to liquid

There are two approaches taking into account the distortion energy or not as implemented in the SPC/E and SPC water models, respectively. The second approach is more common; however, the first was chosen for our model calibration. Therefore, corrections should be made when calculating the absolute energies of the transition from a nonpolar medium to a polar one. It was done in the estimation of the evaporation heat of liquids.

Combining rules

The Lorentz-Berthelot combining rules are widespread in biomolecular modeling. In the proposed model, such rules are applied to hydrogen; the Waldman-Hagler rules are used otherwise [ref]. Such a scheme has little effect on substances consisting of bioelements, but the results significantly differ for heavy elements. If the classical Lorentz-Berthelot rules are required, one must keep in mind that the evaporation heat will be overestimated by a few percents. This is permissible for many purposes; if not, the epsilon of atoms can be reduced accordingly.

Water model

To calculate the free energy of hydration, we used a modified Toukan–Rahman water model from the article. Since this water model was developed without taking into account the vacuum distortion correction, whereas our model takes it into account, there is some inconsistency. Therefore, in our calculations, the distortion correction was taken into account partially only. We used its half value. Corrected values are shown by circles in our graph. Unadjusted values are indicated by diamonds.

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