Check overlapping between merged structures

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.


Please send questions about VMD to the VMD mailing list. Thanks, Axel.