From 36695c020edbeb7a60cf280196273cca8096004e Mon Sep 17 00:00:00 2001
From: ygutier2 <yair.fosado@ed.ac.uk>
Date: Wed, 11 Aug 2021 13:50:32 +0100
Subject: [PATCH] Update README.md

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 # LAMMPS implementation of TopoII using and external code
 
-We model a torsionally relaxed (nicked) DNA plasmid 7.2 kbp-long as a bead-spring polymer made of 1000 beads with bead-size σ=2.5 nm=7.3 bp and connected by finitely extensible springs. The persistence length of the polymer is set to lp = 50 nm. Beads interact via a purely
+We model a torsionally relaxed (nicked) DNA plasmid 7.2 kbp-long as a bead-spring polymer made of 1000 beads with bead-size σ=2.5 nm=7.3 bp and connected by finitely extensible springs. The persistence length of the polymer is set to lp=5σ. 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 k<sub>B</sub>T). For details in the model and the system used we refer the reader to our paper: *D. Michieletto, et al.* "**Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation**".
 
 All the simulation scripts in this repository are set to start from a N=1000 beads thermally equilibrated polymer tied in a 5<sub>1</sub> torus knot. This and other initial configurations are provided inside the folder **0.InitialConfigurations**. The files are written in the correct format to be read by LAMMPS.
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