Dear lammps users
I simulated a cubic box of water molecule. After equilibiration, I wanted to use the this box in another simulation box with bigger boundaries. Unfortunately, I faced “bond atom missing in image check” error. I think this is because of periodic boundary condition and atoms transmitions across the boundaries.
How can I solve this problem?
Thank you in andvance
You can dump the atoms in the smaller periodic box
using “unwrapped” coords. Assuming your image flags
were correct when you created the small system,
you will then get molecules with all the atoms close
to each other in the dump snapshot. How you embed
that snapshot in a larger box is up to you. There is
also a “replicate” command which can be used to
turn a small perioidic box into a bigger one.
Steve
But I want to keep the atoms in the small box coordinate.I want to make the spherical shape of water in biger simulation box.
But I want to keep the atoms in the small box coordinate.I want to make the
spherical shape of water in biger simulation box.
you will have to do this with an external tool based on an unwrapped dump.
LAMMPS doesn't have any feature currently that can do what you want to do.
axel.