> * After this, 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. The random-seed can be used to choose the random position of the initial bead in the topoII section. For the static case the timestep is always 0, indicating that after the initial equilibration the topo II is placed and will not be moved. Finally, it is important to note that **the value of the variable Nbeads in the file Topo2_random_region.c++ must be set by hand to the total number of beads in the system, in this case, it has already been set to 1000**.
> * After this, 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. The random-seed can be used to choose the random position of the initial bead in the topoII section. For the static case the timestep is always 0, indicating that after the initial equilibration the topo II is placed and will not be moved. Finally, it is important to note that **the value of the variable Nbeads in the file Topo2_random_region.c++ must be set by hand to the total number of beads in the system, in this case, it has already been set to 1000**.
> * The output from the simulation is stored in the folder DUMPS.
> * The output from the simulation is stored in the folder DUMPS.
It is important to note that in the section *Parameters*, from line 22 in the lammps script, some variables have been commented using a leading # character. The values in the commented lines correspond to the values set in the original simulations. However we have replaced these values to run a quick check-test.
## Continue a simulation from the last restart file created
## Continue a simulation from the last restart file created
