From: Amir Afshar (
Date: Sat Feb 15 2020 - 10:26:43 CST

Dear Axel,

I have built a setup simulation of water confined by graphene sheets. For
this, I used the "mergemols" in "topotools" option in VMD. Would you please
let me know how I can check and remove if there is any overlap between the
atoms in my merged data file?

I used the Nanotube builder in VMD and generated graphene sheets, then I
added the water box through "topo readlammpsdata" option then merged two

Thank you very much.


Amir Afshar