From: Amir Afshar (
Date: Sat Feb 15 2020 - 17:14:23 CST

Dear Axel,

I went through the instructions given by you in that link for detection and
removal of overlapped atoms in VMD. It seems it only applies for biological
structures with extension of "PDB" or "PSF". I have two Lammps data files
for merging and it doesn't accept the extension of data file I want to
load through " set solute [mol new solute.psf waitfor all]"; It says,
"Could not determine file type for file '......' from its extension, when I
loaded into my VMD TkCosole. May you please let me know how it works for
non-biological structures to build a data file of two merged structures
with no atom overlapping?

Thank you very much.


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
>> --
>> Regards,
>> Amir Afshar
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.