regarding delete_atom

Dear all,

I’m trying to create a void inside a box of a bulk water. After equilibrating the bulk water box, I used region and group command followed by delete_atom command. The keyword was “mol yes”, as I want to delete the entire molecules. But surprisingly all the selected molecules were not deleted so as a consequence my system become non-neutral and pppm throws errors.

For you perusal I’m attaching a short input deck with the log file. Please make your comment.Thanks in advance for your time.

Regards,

input.lmp (1006 Bytes)

log.lammps (1.89 KB)

Dear all,

I'm trying to create a void inside a box of a bulk water. After
equilibrating the bulk water box, I used region and group command followed
by delete_atom command. The keyword was "mol yes", as I want to delete the
entire molecules. But surprisingly all the selected molecules were not
deleted so as a consequence my system become non-neutral and pppm throws
errors.

the "mol yes" options looks at molecule IDs, which may or may not
coincide with what constitutes a molecule.
it is your responsibility, to make sure those are consistent. thus
please look into your data file.

axel.