Re: [ESPResSo-users] Turn off non-bonded interactions between bonded particles

[Florian Fahrenberger]

Dear Matthew,

> Is there a way to turn off the non-bonded interactions between
> bonded particles so that those interactions do not interfere with the
> bonded interaction?

Well, yes and no. It is possible for non-bonded pairwise interactions
like e.g. Lennard-Jones. You can just define the bonded particles as a
certain type and the others as a different one. Like:

for {set i 0} { $i < $num_bonded_particles } {incr i} {
    part $i type 0 pos $posx $posy $posz
}
for {set i $num_bonded_particles} { $i < $all_parts } {incr i} {
    part $i type 1 pos $posx $posy $posz
}
inter 1 1 lennard-jones ...
inter 1 0 lennard-jones ...

This would only create Lennard-Jones interactions between particles of
type 1 and 0, and amongst particles of type 1, but not in between the
particles of type 0.

This will however not easily work for non-pair-interactions like
electrostatics. If a particle is charged, it will always not only see
the free charges in the system but also the charge of its bonded neighbor.

Be aware however that this is on purpose and by design! In physical
systems, particles rarely behave in a way that they might see the charge
of some particles but not the ones of others. If you were to switch off
electrostatics between e.g. polymer beads, you will get unphysical
behaviour for the polymer. So (no matter if this is about electrostatics
or short-ranged interactions), you should definitely think about whether
it is senseful to just turn off an interaction. If you are for example
just bothered by breaking bonds and try to avoid that by tweaking the
force fields, it might be the wrong way to go.

Greetings and I hope I could help,

Florian

-- 
Florian Fahrenberger, Institut für Computerphysik
Allmandring 3, 70569 Stuttgart
Tel: +49-(0)711/685-63594
Fax: +49-(0)711/685-63658