Copy and paste here both the initial configuration generated before "*initial_configuration_ringdsDNA_N1000_T100*" and the LAMMPS executable "lmp_serial_22Aug2018". Then run the lammps script:
You can run simulations here by running in a terminal the comman
./lmp_serial_22Aug2018 -in commands_lammps_dsDNA
./bash.run.sh
Please note that since the simulation starts from an artificial configuration that is far from equilibrium (a circle lying on the xy-plane), at the beggining will appear some warnings (FENE bond too long). The warnings will appear less often once the radius of gyration decreases to a constant value. In addition, we leave some room for the fene bond to change from the average value 0.465 to the maximum value R0=0.6825 set in the lammps script (this is slightly larger than the variations that the real backbone could have) the **warnings** appear because the bond is getting close to this value, and the user **shouldn't worry** about them (the simulation will not crash).
Remember to change the variables LAMMPS and LAMMPSparallel (in this bash file) with the location of your executables. By deffault, the script run a short simulatioun using an artificial initial configuration of a dsDNA 1000 bp long that lies in the x-y plane. In order to use pre-equilibrated configurations of a ring made of 1000 bp, you just need to set the number of helical turns to (94, 100, 106) in line 16 of the bash, to run either: negative, relaxed or positive supercoiled configurations, respectively. You must also uncomment line 20 to run from any of these pre-equilibrated configurations.
Once the simulation finishes you can move the terminal inside the folder "ANALYSIS" and run the bash.analysis.sh file. With this, the total twist (Tw), writhe (Wr) and linking number (Lk=Tw+Wr) will be computed as function of time using the output from the simulation.
