I would echo the suggestion to contact the author, who has posted a tutorial but it lacks a lot of detail, starting from a pre-constructed topology. Note that this force field and its intended use is very different from “normal” GROMACS workflows and you cannot use pdb2gmx for it. Rather, topologies of surfaces and materials should be generated with x2top, which allows for the processing of generic species based solely on distances between the atoms.
We try to simulate nanocoposite comprising the substrate of aluminum oxide (Al2O3) and binder (different polymers (PS, PC, PMMC, etc.)). However, the CLAYFF force field has a limited number of bonded parameters to define the interactions for polymer binder. Is it possible to combine (without any significant problems) the CLAYFF force field with any other atomistic force field to simulate polymer-metal oxide composites in Gromacs?
It is doable to combine Clayff with other ff’s, but it has not really been designed for it. It is typically used with GAFF or OPLS as far as I know. As an alternative, the INTERFACE ff by Hendrik Heinz is supposed to be compatible with CHARMM/CGenFF, but overall it is likely very system dependent, and hence the best approach in mixing inorganic and organic ff’s is likely to try out a few different combinations of them, (like Clayff or Interface ff mixed with GAFF, OPLS, CGenFF), and then see how sensitive the results are to the choice of combination of ff’s.
What forcefield did you have in mind for the polymers? You can contact me directly if you need to see some examples of Clayff/Interface ff’s mixed with organic ff’s.