non periodic


I used both thermo_modify lost ignore, and thermo_modify lost/bond ignore (error was "bond atoms ## missing).
but, that error still pops up.
If I use these command, does Lammps has to ignore the error ?

You misunderstood my response. I wasn’t asking you to use these options, but rather wanted to know, whether you were using them. They can hide bad behavior, and thus should be avoided unless you know exactly what you are doing.

The error message you are seeing is caused by atoms moving very fast between (parallel) subdomains. There are two main reasons for that. A bad geometry, or using “shrink-wrap” boundary conditions with a large vacuum. There are two obvious ways to deal with the latter problem: use “m” boundary instead of “s”, or use a fixed boundary “f” and a reflecting or harmonic wall.
For the former issue, it can help to run a thorough minimization before starting the MD.