From af9e0b0a70ef883d878cb0c4b9ada7416e70f7bf Mon Sep 17 00:00:00 2001 From: ygutier2 <yair.fosado@ed.ac.uk> Date: Wed, 11 Aug 2021 13:31:02 +0100 Subject: [PATCH] Add README.md --- README.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..d102472 --- /dev/null +++ b/README.md @@ -0,0 +1,16 @@ +# 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 +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. + +The position of the TopoII-bound segment can be either: + +* **1.Static**: Meaning that at the begining of the simulation (t=0), the position of the topoII is chosen randomly and then it stays in the same position during the course of the simulation. +* **2.Random Jump**: The positions of the topoII is updated with a certain frequency and it is placed randomly along the contour length of the polymer. +* **3. Jump to maximum density**: The positions of the topoII is updated with a certain frequency and it is placed in the site of maximum density of beads along the contour length of the polymer. + +A brief explanation of the implementation in each of these cases and the scripts to run these simulations are provided inside the corresponding folders in this repository. + +All the LAMMPS scripts have been tested using the current stable-version of LAMMPS (29-October-2020). To built the LAMMPS executables please make sure that the MOLECULE and USER-MISC packages are installed. These are standard packages that come with LAMMPS, and can be enabled before compiling, e.g. with the command: make yes-molecule. -- GitLab