The force-field directory contains files that are used to build Gromacs topologies and parameterize molecules.
The synthetic polymer force field is based on parameters from
Mintis and Mavrantzas (2019), which used the General Amber Force Field (GAFF).
We have converted the tables of parameters into a force field named gaff.ff that can be used with Gromacs.
Small ion parameters, such as sodium, calcium, and chlorine, are taken from the Jungwirth group's ECCR model fittings. Sodium ion parameters are found in:
Kohagen, Miriam, Philip E. Mason, and Pavel Jungwirth. "Accounting for electronic polarization effects in aqueous sodium chloride via molecular dynamics aided by neutron scattering." The Journal of Physical Chemistry B 120.8 (2016): 1454-1460.
Calcium and chlorine ion parameters are found in:
Martinek, Tomas, et al. "Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering." The Journal of chemical physics 148.22 (2018): 222813
Water is modeled using SPC/E, as it offers a good balance of physical performance and computational accuracy. Future work may investigate polarizable water models.
Force field parameter generation is handled by the parameter-generation directory.