Combine the atoms of two different simulations in a new simulation box

Dears,

I need to combine the atoms of two different simulations in a new simulation box .

  • Simulation 1 : 2000 Nanoparticles.
  • Simulation 2 : 200000 solvent particles .

Both simulations are in a rectangular box simulation at the same volume V.

I desire to generate a new simulation box with the same volume V atoms of the nanoparticles and solvent, removing any atom solvent which overlaps with the nanoparticles .

What are the possible ways to do this with Lammps ?

Regards

You can use a text editor to combine the two and use delete_atoms (http://lammps.sandia.gov/doc/delete_atoms.html) command to remove atoms/molecules that overlap.

Ray

Or the read_data command can be used twice (or more)

to input multiple data files. You may still need

to use delete_atoms to get rid of overlaps.

Steve

Dears,

I need to combine the atoms of two different simulations in a new
simulation box .

- Simulation 1 : 2000 Nanoparticles.
- Simulation 2 : 200000 solvent particles .

Both simulations are in a rectangular box simulation at the same volume V.

I desire to generate a new simulation box with the same volume V atoms of
the nanoparticles and solvent, removing any atom solvent which overlaps
with the nanoparticles .

What are the possible ways to do this with Lammps ?

​if there are no bonds in the solvent particle simulation, then you can try
using the read_data command with the option add on the second system. but
that will require some editing of the first data file to leave room for
types etc. then use delete atoms as ray indicated.

if you have some experience with VMD, you can also use Tcl scripting:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal

axel.

Or the read_data command can be used twice (or more)
to input multiple data files. You may still need
to use delete_atoms to get rid of overlaps.

​...and only one of the various data files may have
bonds/angles/dihedrals/impropers.

axel.​