How to delete the leftover atoms within the process of cross-linking of all-atom polymer

Dear lammps users,

As we know, the ‘fix bond/create’ command is very suitable to create the new cross-link bond for bead-spring polymer. However, the problem comes for the all-atom polymer that the leftover atoms should be deleted before or after the cross-link bonds are added into the polymer system. And my question is how to delete the specific atoms within the process of cross-linking of all-atom polymer. I have read the ‘delete_atoms’ command document, which has no information on deleting the individual needless atoms when the new bond are formed. Thanks for your advices and comments.

Best regards!

D. Chai


An effective binding process in which atomic-level compounds are removed from
the system should be designed in addition to fix bond/create.

fix bond/create only adds bonds (and angles, dihedrals and impropers if you use
the appropriate settings) and does not remove them.



I’ll add that the delete_atoms (or delete_bonds) cannot
work in tandem with fix bond/create b/c the fix operates
periodically during a run. The 2 delete commands perform
a one-time operation in between runs.

There is a fix evaporate command which can remove atoms
or molecules from a system during a run.

I agree the bond creation/deletion due to “reactions” (modeled

at the empirical MD level) could be made a lot more general.
I.e. the fix bond/create and fix bond/break commands are
a starting point, but feel free to make suggestions as to
how they could be enhanced.