> 1.- The number of independent simulations to run. This is done by running the same lammps script (run.lam) with the same initial configuration (Eq.5_1.N1000.data) several times. The results from these simulations are stored into the folders REP1, REP2, ..., REPn.
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> 2.- The instructions to produce the file *parameters.dat* which contains different random seeds that are used to produce independent simulations.
### The run.lam script
> 1.- The initial configuration contains a bead-and-spring polymer made by 1000 beads of type 1 that repeal each other via a purely repulsive LJ potential. Consecutive beads are connected via FENE bonds.
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> 2.- The simulation is run for 3000000 timesteps. Then a restart file *dataRestart.Run.R1.0* is created.
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> 3.- We use the program **Topo2_random_region.c++** to place the topo II randomly along the DNA contour length. The arguments required by this programs are: timestep, input-file, output-file, random-seed. The input-file (*dataRestart.Run.R1.0*) is the restart file that comes from the previous equilibration. The output-file (*newdataRestart.Run.R1.0*) contains the position of the topo II represented by 50 beads of type 4 that interact through a soft potential, allowing strand crossing. In the static case the timestep is always 0, indicating that after the initial equilibration the topo II is placed. Finally, it is important to note that **the value of the variable Nbeads in the c++ must be set by hand to the total number of beads in the system, this is 1000**.
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> 4.- The output from the simulation is stored in the folder DUMPS
