@@ -14,23 +14,17 @@ The bash scripts provided in this folder contain the instructions to run 64 inde
In this file:
* It is assumed that the simulations are run in a cluster with 64 processors available. If this is not the case, users can change the value of the variable *ncpu=64* according to their needs. This variable also sets the number of independent simulations to run. The results from these simulations are stored into the folders REP1, REP2, ..., REP64. Each of the 64 simulations:
* Runs in serial.
* Starts from the same initial configuration, *Eq.5_1.N1000.data* and runs for an equilibration time before introducing the topoII region.
* There are instructions to produce the file *parameters.dat* which contains different random seeds that are used to produce independent simulations.
> * It is assumed that the simulations are run in a cluster with 64 processors available. If this is not the case, users can change the value of the variable *ncpu=64* according to their needs. This variable also sets the number of independent simulations to run. The results from these simulations are stored into the folders REP1, REP2, ..., REP64. Each of the 64 simulations:
> * Runs in serial.
> * Starts from the same initial configuration, *Eq.5_1.N1000.data* and runs for an equilibration time before introducing the topoII region.
> * There are instructions to produce the file *parameters.dat* which contains different random seeds that are used to produce independent simulations.
### The run.lam script
* The initial configuration data file contains a bead-and-spring polymer made by 1000 beads of type 1. In the LAMMPS script a Lennard Jones repulsive potential is set between these type of particles so they can't overlap or cross through each other. Consecutive beads are connected via FENE bonds.
* The simulation is run for *run1=1000000 timesteps*. Then a restart file *dataRestart.Run.R1.0* is created.
* 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 initial configuration data file contains a bead-and-spring polymer made by 1000 beads of type 1. In the LAMMPS script a Lennard Jones repulsive potential is set between these type of particles so they can't overlap or cross through each other. Consecutive beads are connected via FENE bonds.
> * The simulation is run for *run1=1000000 timesteps*. Then a restart file *dataRestart.Run.R1.0* is created.
> * 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.
