NFsim error trying to bond two already bound sites when (intramolecular) ring closure reaction is allowed.
## title: BLBR_error.bngl
# description: Ring closure with a disjoint pattern exposes a bug in NFsim. The seed
# has been set to make this model behavior deterministic.
setOption("SpeciesLabel","HNauty");
begin parameters
kp1 1
km1 1
kp2 1
km2 1
kp3 1
km3 1
R0 1000
L0 1000
end parameters
begin species
R(r,r) R0
L(l,l) L0
end species
begin reaction rules
# Ligand addition
R(r) + L(l,l) <-> R(r!1).L(l!1,l) kp1,km1
# Chain elongation
R(r) + L(l,l!+) <-> R(r!1).L(l!1,l!+) kp2,km2
# Ring closure
R(r).L(l) <-> R(r!1).L(l!1) kp3,km3
end reaction rules
simulate({method=>"nf",seed=>916749345,t_end=>10,n_steps=>1000,get_final_state=>1})
NFsim error trying to bond two already bound sites when (intramolecular) ring closure reaction is allowed.