Model interaction potentials - steventopper/TransRot GitHub Wiki

The TransRot project is compatible with a range of pairwise additive model potentials, and some of them are described here. Of course, our implementation is limited to rigid-body assumptions and molecules which have internal rotational flexibility should not be implemented in TransRot without due caution.

1. We have made extensive use of the Jorgensen groups' OPLS-AA, OPLS-UA (1997), and TIP3P/TIP4P/TIP5P models for project work, which are implemented in their powerful BOSS Monte Carlo simulation software, as well as within the Tinker project, a powerful suite for molecular modeling. See here: (https://jorgensenresearch.com/software) and here: https://dasher.wustl.edu/tinker/ . Our default combination rules use geometric means for $C_{ij}$ and $D_{ij}$, and so atom type parameters from these models can be used directly.

2. The TraPPE force field from the Siepmann group does not use the same combination rules as TransRot; TraPPE uses the Lorentz-Berthelot combination rules, whereas TransRot defaults to the use of geometric means. However, TransRot's default combination rules can be easily overridden and the correct pair interactions provided explicitly. The TraPPE parameters and correct rules for a number of molecules can be obtained here: (http://trappe.oit.umn.edu/#param_content)

3. Any system-specific pairwise interaction potential that is of the general form expected by TransRot can be implemented, including the use of custom interaction parameters. One note of caution is that if the uncorrected Buckingham- Exp6 potential is used without the addition of a custom short-ranged D/r^12 repulsion term, it is possible for short-ranged interactions to diverge during a simulation if two particles move too close together. This is an unfortunate feature of the uncorrected Buckingham-Exp6 model, and not a "bug." Also, as noted above the default rules used for combinations can be overridden if needed for a specific system.