- Prepare initial configutation
- go to "INIT"
- open the kDNA image (called crop.tif)
- create a binar mask w threshold > 65 (estimated using background mean intensity + 3 times its standard deviation)
- save thresholded image as skel.tif
- use image calcuator to "AND" original image and binarised one
- save as TIFF
- save as data matrix "matrix_w_intensity.txt"
- Map matrix of intensities to phantom beads
- open bash.sh to set the parameters
- use bas.sh as "./bash.sh" in terminal to create initial configuration
- in gnuplot type p "kdna.afm.data" i 0 u 4:5:3 palette to visualise initial configuration
- Run LAMMPS simulation
- go to "RUN"
- create a "parameters.dat" file with random seeds, e.g. variable seed1 equal 4414 variable seed2 equal 1123 variable seed3 equal 9091
- run as
~/lmp_mpi -in run.lam from terminal