@@ -11,6 +11,9 @@ The position of the TopoII-bound segment can be either:
***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.
