From: Frank Zack (
Date: Mon Oct 19 2015 - 08:34:16 CDT

Hi all,
i was wondering if it its possible to delete atoms and save the new configuration again as lammps-data-file.
I've simulated crosslinking of pp via organosilane-bridges in lammps. Before a new bond is formed, I tried to remove an OH-group at one of the 'linking sites' using the delete command in lammps. Unfortunately, only the oxygen is deleted but not the hydrogen. The non-bonded hydrogen-atom then flies around my simulation box and blows it up (Im not sure why, maybe because of the unsaturated charge?).
Now im trying to write a tcl-script to delete all non-bonded hydrogens again. But Im not sure whats the simplest way to do so.acc
My approach is just looping through all hydrogens and check if they are bonded or not using topo-tools.For this purpose I need to remove these hydrogens from my "set sel [atomselect "top all]". How can I accomplish this, or is there a more straighforward way?