# Topo2 implementation into LAMMPS with external code
Here you will find the c++ codes and LAMMPS scripts to run simulations of the topological relaxation of bead-spring polymers (which are initially knotted) by the action of a simulated Topo2 protein.
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We model a torsionally relaxed (nicked) DNA plasmid 3.6 kbp-long as a bead-spring polymer made of 500 beads with size σ = 2.5nm = 7.3 bp and connected by finitely extensible springs and persistence length lp = 50 nm. Beads interact via a purely
steric Lennard-Jones repulsion while the TopoII-bound segment is modelled as a 50 beads (L = 360 bp)-long segment displaying soft interactions with the other beads thereby allowing the TopoII-bound segment to undergo strand-crossing with a small energy penalty (2 kB T)
