From: Amir Afshar (
Date: Sat Feb 15 2020 - 15:18:32 CST

Dear Axel,

Thank you. I just found the link you sent to me. As it shows, It was
suggested for biological matters like as protein structures. I have
graphene sheets build with VMD and water molecules in my simulation box
that merged via topotools in VMD. May you please let me know if this method
also works for building non-biological structure with non overlapped atom

Thank you.

On Sat, Feb 15, 2020 at 11:10 AM Axel Kohlmeyer <> wrote:

> On Sat, Feb 15, 2020 at 11:53 AM Amir Afshar <>
> wrote:
>> 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
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.