Initial configuration of atoms in PDB

Hi users

I’m working on crystals and want to simulate a calcite slab.

When making its structure in Material Studio, some atoms (herein, oxygens of carbonates) being placed out of periodic boundary box.
What would happen while running such case in LAMMPS?
Should I place all atoms in the box?

See the following image
image.png


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Hi users

I'm working on crystals and want to simulate a calcite slab.

When making its structure in Material Studio, some atoms (herein, oxygens
of carbonates) being placed out of periodic boundary box.
What would happen while running such case in LAMMPS?
Should I place all atoms in the box?

http://lammps.sandia.gov/doc/read_data.html

image.png