Instructions

To simulate the load simulation set k_stiff parameter to zero

Run 1st equilibriumstiff.py, alat = 55,100,150,250 for n_beads = 21,40,62,84 respectively. Refer thesis for other inputs
Then run walladdstiff.py to add walls
Then graft the wall to gel using graftequilstiff.py and equilibrate
now use pullgraftgelstiff.py to pull the gel with a constant force
run production.py to run contraction simulations with parameters : dof = 0 cforce in the list k = 200 k1= 200 kang = 1000 kdihed = 300 no_beads = 21 Torque = 35.0 sample = 1 rotperiod = 20000 relaxationp = 20000 langperiod = 60000000 Ktors = 600

Run 1st ucell_moiSideStiffFree.py to create gel , alat = 55,100,150,250 for n_beads = 21,40,62,84 respectively. Refer thesis for other inputs.
After initialization run Freestiffgel.py for relaxing the gel
Run FreeStiffproduction.py for contraction
Continue contraction using continueproduction.py $1 600 $3 20000 20000 759.375 0 200 200 $2 parameters: k = 200 k1=200 Ktors = 600 kmax = 759.375

no_beads = 21 or 40 or 62 or 84 sample = 1 k_constraint =10000 rotperiod = 20000 relaxationp = 20000 langperiod = 0
600 cycles of contraction already defined within the code