From: Giacomo Fiorin (
Date: Sat Feb 15 2020 - 11:14:47 CST

Hello Amir, you can probably take inspiration from the many scripts in the
VMD website used to set up protein simulations. In those, selections of
overlapping atoms are used to instruct the psfgen program to delete the
corresponding atoms from the system being prepared.

You probably won't use psfgen for a LAMMPS data file, but you should be
able to pass a custom selection to the "topo" command to tell it to save a
data file that contains only non-overlapping atoms.


On Sat, Feb 15, 2020 at 11:54 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
> --
> Regards,
> Amir Afshar

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD