units real atom_style hybrid charge angle #read_restart initial read_data ts.txt reset_timestep 0 timestep 2 variable a loop 60 group rodions1 type 1 # Center of left DNA group rodions2 type 2 # Center of right DNA group rods type 1 2 mass 1 20 mass 2 20 pair_style hybrid/overlay lj/cut/coul/long 10 coul/diel 10 gauss 18 #Coulombic interactions #----------------------------------------------------------------------------------- pair_coeff 1 1 lj/cut/coul/long 0.0 0 # Rodion1-Rodion1 pair_coeff 1 2 lj/cut/coul/long 0.1553 3.68 # Rodion1-Rodion2 pair_coeff 2 2 lj/cut/coul/long 0.0 0 # Rodion2-Rodion2 #------------------------------------------------------------------------------------ pair_coeff 1 2 coul/diel 66.8 3.68 1.0 # Rodion1-Rodion2 #------------------------------------------------------------------------------------- # Solvation shells pair_coeff 1 1 gauss 0.0 1.0 # Rodion1-Rodion1 pair_coeff 1 2 gauss 5 3.5 0.5 # Rodion1-Rodion2 pair_coeff 2 2 gauss 0.0 1.0 # Rodion2-Rodion2 #-------------------------------------------------------------------------------------- bond_style harmonic bond_coeff 1 500.0 1.0 #kspace_style pppm 0.0001 kspace_style ewald 0.000000001 dielectric 72 neighbor 2.0 bin fix 2 rodions1 store/force fix 2b rodions2 store/force fix 3 rodions1 setforce 0.0 0.0 0.0 fix 4 rodions2 setforce 0.0 0.0 0.0 compute 11 rodions1 reduce sum f_2[1] compute 14 rodions2 reduce sum f_2b[1] #compute 7 freeions temp variable d equal x[11]-x[1] fix 6 all ave/time 10 1 10 c_11 c_14 file alaki.txt fix 8 all ave/time 10000000 1 10000000 c_11 c_14 file fc.txt ave running thermo 10000 thermo_style custom step temp dump 1 rods custom 10000000 rods id type x y z run 0 #write_restart result$a label loop reset_timestep 0 timestep 1 fix 13 rodions1 move linear 0.00125 0 0 units box fix 14 rodions2 move linear -0.00125 0 0 units box run 50 unfix 13 unfix 14 unfix 6 #unfix 8 undump 1 reset_timestep 0 timestep 2 velocity rods set 0.0 0.0 0.0 units box fix 6 all ave/time 10 1 10 c_11 c_14 file gc_$a.txt dump 1 rods custom 10000000 rods.$a id type x y z run 10 #write_restart result$a next a jump in5.simple loop