I am looking for a script to construct an amoprhphous cell with polymer chains as well as gas molecules to avoid ring catenation. After the construction I want to stepwise delete the gas molecules to end with a cell only containing my polymer chains. I tried deleting the gas by hand, but that changes the trajectory and then I can't use forcite anymore. Does anyone have a script that could save my problem? I'm doing my master's thesis, so unfortunately I don't have the time to figure out scripting by myself.
Hi Jason, thank you for your answer! I solved the trajectroy Problem last week exactly as you suggested. I managed to delete the molecules after converting the file, but now my density is too low. But I'm gonna try packing many different cells and hopefully get a successful one soon. The reason I am trying to do it this way is a paper by Chi Hoon Park et al. which I wanted to reproduce in order to compare the results. I guess I just have to trust the program and maybe start with my own models, since I'm not really getting anywhere with this approach.