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-# Kdna Afm Md
+1. Prepare initial configutation 
 
-MD simulations in LAMMPS based on AFM data
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+- 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"
+
+2. 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 
+
+3. 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