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 structures.
Thank you very much.
Regards