Hi,

I have been trying to build a cell (not sure if I can call it amorphous) of two polystyrene chains (PS) and one graphene sheet in toluene solvent. I wanted to start with having graphene in the center of the cell and a PS chain on top while the other at the bottom of graphene sheet. I tried amorphous construction and that simply places molecules randomly in the simulation cell. 

So, I build an amorphous cell and created sets of graphene sheet and PS chains so I can select and move them separately. I can move them and arrange as needed but this leads to some overlapping atoms. To go ahead with the simulation, I must delete overlapping toluene fragments (toluene fragments of which any one atom overlaps or is very close to either PS chain or graphene sheet). Although I can understand and edit MS Perl scripts, I still do not have enough expertise to write a complete script to achieve my objective.

Please suggest the possible ways I can achieve this.

I have went searched for existing posts with the keyword including "overlapping", "remove overlap", "delete overlap", "remove overlapping atoms" etc. but no post seems to be relevant.

Thank you!