VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 19 2015 - 09:25:03 CDT

On Mon, Oct 19, 2015 at 9:34 AM, Frank Zack <frankzack123_at_remove_yahoo.de>
wrote:

> 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?).
>

​if your system is properly set up in lammps, i.e. molecules are identified
by proper molecule ids, it should be no problem to delete that stray
hydrogen using the "mol yes" flag.

​axel.​

> 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?
>
> regards,
> frank.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.