# System units real atom_style full dimension 3 boundary p p p #Read data of the system read_data combined_data.data group water type 12 13 group polymer type 1 2 3 4 5 6 7 8 9 10 11 #Pair Styles & co_eff pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 pair_modify mix arithmetic pair_coeff 1 1 lj/charmm/coul/long 0.041731 3.879998 #CA0 pair_coeff 2 2 lj/charmm/coul/long 0.100354 3.695002 #CA1 pair_coeff 3 3 lj/charmm/coul/long 0.000994 6.400003 #CH0 pair_coeff 4 4 lj/charmm/coul/long 0.091411 3.950004 #CH2 pair_coeff 5 5 lj/charmm/coul/long 0.194746 3.749998 #CH3 pair_coeff 6 6 lj/charmm/coul/long 0.119232 3.55 #CL0 pair_coeff 7 7 lj/charmm/coul/long 0.059616 3.7 #CS0 pair_coeff 8 8 lj/charmm/coul/long 0.139104 2.599999 #HL@OA0 pair_coeff 9 9 lj/charmm/coul/long 0.119232 2.949997 #NL0 pair_coeff 10 10 lj/charmm/coul/long 0.139104 2.599999 #OA0 pair_coeff 11 11 lj/charmm/coul/long 0.059616 3.7 #TL@CS0 pair_coeff 12 12 lj/charmm/coul/long 0.0460 0.4000 #Hspc pair_coeff 13 13 lj/charmm/coul/long 0.0836 1.1226 #Ospc #Bond style & Co_eff bond_style hybrid harmonic bond_coeff 1 harmonic 478.4 1.387# 1 CA0-CA0 bond_coeff 2 harmonic 478.4 1.387# 2 CA0-CA1 bond_coeff 3 harmonic 323.5 1.513 # 3 CA0-CH0 bond_coeff 4 harmonic 404.1 1.44 # 4 CA0-CL0 bond_coeff 5 harmonic 478.4 1.387 # 5 CA0-CS0 bond_coeff 6 harmonic 478.4 1.387 # 6 CA0-TL@CS0 bond_coeff 7 harmonic 478.4 1.387 # 7 CA1-CS0 bond_coeff 8 harmonic 303.1 1.535 # 8 CH0-CH2 bond_coeff 9 harmonic 303.1 1.535 # 9 CH0-CH3 bond_coeff 10 harmonic 1014.5 1.138 # 10 CL0-NL0 bond_coeff 11 harmonic 478.4 1.387 # 11 CS0-CS0 bond_coeff 12 harmonic 372.4 1.373 # 12 CS0-HL@OA0 bond_coeff 13 harmonic 372.4 1.373 # 13 CS0-OA0 bond_coeff 14 harmonic 478.4 1.387 # 14 TL@CS0-TL@CS0 bond_coeff 15 harmonic 600 1.00 #Hspc-Ospc #Angle style & Co_eff angle_style hybrid harmonic angle_coeff 1 harmonic 67.18 119.97 # CA0-CA0-CA1 angle_coeff 2 harmonic 63.66 112.26 # CA0-CA0-CH0 angle_coeff 3 harmonic 67.18 119.97 # CA0-CA1-CS0 angle_coeff 4 harmonic 63.84 120.63 #CA0-CH0-CA0 angle_coeff 5 harmonic 63.25 112.09 #CA0-CH0-CH2 angle_coeff 6 harmonic 63.25 112.09 #CA0-CH0-CH3 angle_coeff 7 harmonic 63.14 180.0 #CA0-CL0-NL0 angle_coeff 8 harmonic 67.18 119.97 #CA0-CS0-CS0 angle_coeff 9 harmonic 69.79 119.2 #CA0-CS0-OA0 angle_coeff 10 harmonic 67.18 119.97 #CA0-TL@CS0-TL@CS0 angle_coeff 11 harmonic 63.84 120.63 #CA1-CA0-CH0 angle_coeff 12 harmonic 67.18 119.97 #CA1-CS0-CS0 angle_coeff 13 harmonic 69.79 119.2 #CA1-CS0-HL@OA0 angle_coeff 14 harmonic 67.18 119.97 #CA1-CS0-OA0 angle_coeff 15 harmonic 63.21 110.63 #CH0-CH2-CH0 angle_coeff 16 harmonic 63.21 110.63 #CH2-CH0-CH2 angle_coeff 17 harmonic 63.21 110.63 #CH2-CH0-CH3 angle_coeff 18 harmonic 63.21 110.63 # CH3-CH0-CH3 angle_coeff 19 harmonic 65.86 120.0 #CL0-CA0-CS0 angle_coeff 20 harmonic 65.86 120.0 #CL0-CA0-TL@CS0 angle_coeff 21 harmonic 67.18 119.97 #CS0-CA0-CS0 angle_coeff 22 harmonic 67.18 119.97 #CS0-CA0-TL@CS0 angle_coeff 23 harmonic 69.79 119.2 # CS0-CS0-HL@OA0 angle_coeff 24 harmonic 69.79 119.2 # CS0-CS0-OA0 angle_coeff 25 harmonic 63.31 119.95 # CS0-OA0-CS0 angle_coeff 26 harmonic 75 109.47 #Hspc-Ospc-Hspc #Dihedral style & Co_eff dihedral_style hybrid fourier dihedral_coeff 1 fourier 1 3.625 -1 2 # CA0-CA0-CA1-CS0 dihedral_coeff 2 fourier 1 0.0 -1 2 # CA0-CA0-CH0-CA0 dihedral_coeff 3 fourier 1 0.0 -1 2 # CA0-CA0-CH0-CH2 dihedral_coeff 4 fourier 1 0.0 -1 2 # CA0-CA0-CH0-CH3 dihedral_coeff 5 fourier 1 3.625 -1 2 # CA0-CA1-CS0-CS0 dihedral_coeff 6 fourier 1 3.625 -1 2 # CA0-CA1-CS0-HL@OA0 dihedral_coeff 7 fourier 1 0.0 -1 2 # CA0-CA1-CS0-OA0 dihedral_coeff 8 fourier 1 0.15555 -1 2 # CA0-CH0-CH2-CH0 dihedral_coeff 9 fourier 1 3.625 -1 2 # CA0-CS0-CS0-CA0 dihedral_coeff 10 fourier 1 3.625 -1 2 # CA0-CS0-CS0-OA0 dihedral_coeff 11 fourier 1 3.625 -1 2 # CA0-CS0-OA0-CS0 dihedral_coeff 12 fourier 1 3.625 -1 2 # CA0-TL@CS0-TL@CS0-CA0 dihedral_coeff 13 fourier 1 3.625 -1 2# CA1-CA0-CA0-CA1 dihedral_coeff 14 fourier 1 3.625 -1 2 # CA1-CA0-CA0-CH0 dihedral_coeff 15 fourier 1 3.625 -1 2 # CA1-CA0-CH0-CA0 dihedral_coeff 16 fourier 1 0.0 -1 2 # CA1-CA0-CH0-CH2 dihedral_coeff 17 fourier 1 0.0 -1 2 # CA1-CA0-CH0-CH3 dihedral_coeff 18 fourier 1 3.625 -1 2 # CA1-CS0-CS0-CA1 dihedral_coeff 19 fourier 1 3.625 -1 2 # CA1-CS0-CS0-HL@OA0 dihedral_coeff 20 fourier 1 3.625 -1 2 # CA1-CS0-CS0-OA0 dihedral_coeff 21 fourier 1 0.9 -1 2 # CA1-CS0-OA0-CS0 dihedral_coeff 22 fourier 1 3.625 -1 2 # CH0-CA0-CA0-CH0 dihedral_coeff 23 fourier 1 3.625 -1 2 # CH0-CA0-CA1-CS0 dihedral_coeff 24 fourier 1 0.1555 -1 2 # CH2-CH0-CH2-CH0 dihedral_coeff 25 fourier 1 0.1555 -1 2 # CH3-CH0-CH2-CH0 dihedral_coeff 26 fourier 1 3.625 -1 2 # CL0-CA0-CS0-CS0 dihedral_coeff 27 fourier 1 3.625 -1 2 # CL0-CA0-CS0-OA0 dihedral_coeff 28 fourier 1 3.625 -1 2 # CL0-CA0-TL@CS0-TL@CS0 dihedral_coeff 29 fourier 1 0.0 -1 2 # CS0-CA0-CL0-NL0 dihedral_coeff 30 fourier 1 0.9 -1 2 # CS0-CA0-CS0-CS0 dihedral_coeff 31 fourier 1 0.9 -1 2# CS0-CA0-CS0-OA0 dihedral_coeff 32 fourier 1 3.625 -1 2 # CS0-CA0-TL@CS0-TL@CS0 dihedral_coeff 33 fourier 1 3.625 -1 2 #CS0-CS0-OA0-CS0 dihedral_coeff 34 fourier 1 3.625 -1 2 # HL@OA0-CS0-CS0-HL@OA0 dihedral_coeff 35 fourier 1 3.625 -1 2 # OA0-CS0-CS0-OA0 dihedral_coeff 36 fourier 1 0.0 -1 2 # TL@CS0-CA0-CL0-NL0 dihedral_coeff 37 fourier 1 3.625 -1 2 # TL@CS0-CA0-CS0-CS0 dihedral_coeff 38 fourier 1 3.625 -1 2 #TL@CS0-CA0-CS0-OA0 special_bonds amber improper_style none #Define kspace & rattale kspace_style pppm 0.0001 fix fRattleSPCE water rattle 0.0001 10 100 b 1 a 1 min_style sd minimize 1.0e-3 1.0e-3 1000 100000 min_style cg min_modify line quadratic minimize 1.0e-4 1.0e-4 1000 100000 # Define velocity & ensemble velocity all create 273.0 5463576 fix 1 all nvt temp 273.0 273.0 100.0 # timestep timestep 1.0 # Tracking the simulation thermo_style custom step temp press etotal density pe ke thermo 1000 dump d10 all custom 1000 system*.cfg id type x y z # Run command run 10000 write_data system_check.data