# see the documentation for a description of the LJ units units real atom_style full #angle_style cosine #bond_style harmonic boundary p p p region all block -150.00 150.00 -500.00 500.00 -150.00 150.00 create_box 4 all #read_data nanotube.data add merge molecule 1 molecule_2.template timestep 0.01 region whole block -150.00 150.00 -500.00 500.00 -150.00 150.00 region left block -150.00 150.00 -500.00 -50.00 -150.00 150.00 region right block -150.00 150.00 50.00 500.00 -150.00 150.00 region tube block -50.00 50.00 -50.00 50.00 -50.00 50.00 create_atoms 0 random 100 5321 whole mol 1 55251 units box pair_style morse 20 pair_coeff 1 1 0.0 1.0 0.0 # the pore atoms do not self-interact pair_coeff 1 2 0.1 0.24 11 13 # protein-pore interaction pair_coeff 1 3 0.1 0.24 11 13 # protein-pore interaction pair_coeff 1 4 0.1 0.24 11 13 # protein-pore interaction pair_coeff 2 4 2.73 0.24 11 20 # protein-protein interaction pair_coeff 2 3 0.1 0.24 11 13 pair_coeff 3 4 0.1 0.24 11 13 pair_coeff 2 2 0.1 0.24 11 13 pair_coeff 3 3 0.1 0.24 11 13 pair_coeff 4 4 0.1 0.24 11 13 mass * 1397.21 #group pore type 1 #fix freeze pore setforce 0 0 0 group protein type 2:4:1 #thermo_modify lost ignore velocity protein create 310 87287 loop geom neighbor 2.0 bin neigh_modify delay 0 every 20 check no # minimize the energy minimize 1.0e-4 1.0e-6 100 1000 # default timestep 0.005 tau fix 1 protein rigid/nve/small molecule langevin 310 310 700 498094 #fix 1 protein rigid/nve/small molecule #compute 1 protein temp #compute_modify 1 dynamic yes #compute msd protein msd com yes #compute_modify msd dynamic yes #Converting units of diffusion coef from A^2/fs to cm^2/s (cm^2/s = 10*A^2/fs) #variable twopoint equal c_msd[4]/6/(10*step*dt+1.0e-6) #fix 9 protein vector 10 c_msd[4] #variable fitslope equal slope(f_9)/6/(10*10*dt) #compute num1 protein property/atom mass #compute num2 protein reduce/region left sum c_num1 #compute num3 protein reduce/region right sum c_num1 #compute num4 protein reduce/region tube sum c_num1 #variable mleft equal c_num2 #variable mright equal c_num3 #variable mtube equal c_num4 #thermo_style custom step c_num3 c_num2 c_num4 c_1 c_msd[4] v_twopoint v_fitslope #thermo_modify lost ignore dump trj all xyz 1000 traj.xyz thermo 1000 run 10000000