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ulliulli 

Script for amorphous cell construction

Hello everyone,

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. 

Thanks in advance!
Jason DeJoannisJason DeJoannis
Hi Ulli,

To convert a trajectory to an XSD, you can either copy-paste to a new XSD or use File | Export.

Now there are better ways to avoid ring catenation:
  1. Use the new (MS2018) "restrain rings" feature in the Options dialog. This shrinks the rings down a bit during packing.
  2. Pack at low density and ramp to target
  3. Pack many different frames and use the ones that are successful.
  4. All of the above at once.
Best,
Jason
ulliulli
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.

Best,
Ulli