I am trying to equilibrate a system of silicon(diamond structure) and amorphous polyaniline. I created the structure in xenoview using pcff forcefield.
I am using sw for silicon, lj/class2/coul/long for polymer and lj/cut for interaction between Si and individual atoms of the polymer. When I simulated only the silicon box using sw, the diamong structure is preserved and , lj/class2/coul/long is known to work well with polymers. However, when used together in this hybrid scheme, the silicon lattice crumbles and shrinks and forms an amorphous block.
Here is the relevant part of the script: