# System units real atom_style full dimension 3 boundary p p p #Read data of the system read_data polymer.lmps extra/atom/types 2 extra/bond/types 1 extra/angle/types 1 #polymer have 11 atom types read_data solvent.lmps add append offset 2 1 1 0 0 #water have 2 atom types 1 bond and angle types #Re-initialize water mass mass 12 15.9994 mass 13 1.0008 #spearate the polymer & water group group solvent type 12 13 group polymer type 1 2 3 4 5 6 7 8 9 10 11 #Pair Styles & co_eff special_bonds amber pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 lj/cut/coul/long 10.0 pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 pair_coeff 1 1 lj/charmm/coul/long 0.139104 2.599999 pair_coeff 2 2 lj/charmm/coul/long 0.059616 3.7 pair_coeff 3 3 lj/charmm/coul/long 0.100354 3.695002 pair_coeff 4 4 lj/charmm/coul/long 0.041731 3.879998 pair_coeff 5 5 lj/charmm/coul/long 0.000994 6.400003 pair_coeff 6 6 lj/charmm/coul/long 0.091411 3.95000 pair_coeff 7 7 lj/charmm/coul/long 0.194746 3.749998 pair_coeff 8 8 lj/charmm/coul/long 0.059616 3.7 pair_coeff 9 9 lj/charmm/coul/long 0.119232 3.55 pair_coeff 10 10 lj/charmm/coul/long 0.119232 2.949997 pair_coeff 11 11 lj/charmm/coul/long 0.139104 2.599999 pair_coeff 12 12 lj/cut/coul/long 0.1554164124 3.1655200879 #O-O pair_coeff 13 13 lj/cut/coul/long 0.0000000000 0.000000000 #H-H #Bond style & Co_eff bond_style hybrid harmonic bond_coeff 1 harmonic 372.4 1.373 bond_coeff 2 harmonic 478.4 1.387 bond_coeff 3 harmonic 478.4 1.387 bond_coeff 4 harmonic 478.4 1.387 bond_coeff 5 harmonic 478.4 1.387 bond_coeff 6 harmonic 303.1 1.535 bond_coeff 7 harmonic 323.5 1.513 bond_coeff 8 harmonic 303.1 1.535 bond_coeff 9 harmonic 478.4 1.387 bond_coeff 10 harmonic 478.4 1.387 bond_coeff 11 harmonic 478.4 1.387 bond_coeff 12 harmonic 404.1 1.44 bond_coeff 13 harmonic 1014.5 1.138 bond_coeff 14 harmonic 372.4 1.373 bond_coeff 15 harmonic 600 1.0000 # for water #Angle style & Co_eff angle_style hybrid harmonic angle_coeff 1 harmonic 63.31 119.95 angle_coeff 2 harmonic 69.79 119.2 angle_coeff 3 harmonic 69.79 119.2 angle_coeff 4 harmonic 67.18 119.97 angle_coeff 5 harmonic 63.21 110.63 angle_coeff 6 harmonic 63.25 112.09 angle_coeff 7 harmonic 63.21 110.63 angle_coeff 8 harmonic 63.21 110.63 angle_coeff 9 harmonic 63.66 112.26 angle_coeff 10 harmonic 63.21 110.63 angle_coeff 11 harmonic 63.25 112.09 angle_coeff 12 harmonic 63.21 110.63 angle_coeff 13 harmonic 63.21 110.63 angle_coeff 14 harmonic 63.21 110.63 angle_coeff 15 harmonic 63.66 112.26 angle_coeff 16 harmonic 67.18 119.97 angle_coeff 17 harmonic 67.18 119.97 angle_coeff 18 harmonic 65.86 120.0 angle_coeff 19 harmonic 65.86 120.0 angle_coeff 20 harmonic 67.18 119.97 angle_coeff 21 harmonic 69.79 119.2 angle_coeff 22 harmonic 63.14 180.0 angle_coeff 23 harmonic 69.79 119.2 angle_coeff 24 harmonic 69.79 119.2 angle_coeff 25 harmonic 67.18 119.97 angle_coeff 26 harmonic 75 109.4700 #for water #Dihedral style & Co_eff dihedral_style hybrid fourier dihedral_coeff 1 fourier 1 0.9 -1 2 # CS0,CS0,OA0,CS0 dihedral_coeff 2 fourier 1 0.9 -1 2 # CS0,CS0,OA0,CS0 dihedral_coeff 3 fourier 1 3.625 -1 2 # OA0,CS0,CS0,OA0 dihedral_coeff 4 fourier 1 3.625 -1 2 # OA0,CS0,CS0,CA1 dihedral_coeff 5 fourier 1 3.625 -1 2 # CA1,CS0,CS0,CA1 dihedral_coeff 6 fourier 1 3.625 -1 2 # CA0,CA0,CA1,CS0 dihedral_coeff 7 fourier 1 3.625 -1 2 # CH0,CA0,CA1,CS0 dihedral_coeff 8 fourier 1 3.625 -1 2 # CA1,CA0,CA0,CA1 dihedral_coeff 9 fourier 1 3.625 -1 2 # CA1,CA0,CA0,CH0 dihedral_coeff 10 fourier 1 3.625 -1 2 # CH0,CA0,CA0,CH0 dihedral_coeff 11 fourier 1 3.625 -1 2 # CS0,CS0,CA1,CA0 dihedral_coeff 12 fourier 1 3.625 -1 2 # OA0,CS0,CA1,CA0 dihedral_coeff 13 fourier 1 0.15555 1 3 # CH0,CH2,CH0,CA0 dihedral_coeff 14 fourier 1 0.15555 1 3 # CH0,CH2,CH0,CH3 dihedral_coeff 15 fourier 1 0.0 1 2 # CA0,CA0,CH0,CH2 dihedral_coeff 16 fourier 1 0.0 1 2 # CA0,CA0,CH0,CH3 dihedral_coeff 17 fourier 1 0.0 1 2 # CA1,CA0,CH0,CH2 dihedral_coeff 18 fourier 1 0.0 1 2 # CA1,CA0,CH0,CH3 dihedral_coeff 19 fourier 1 0.15555 1 3 # CH0,CH2,CH0,CH2 dihedral_coeff 20 fourier 1 0.0 1 2 # CA0,CA0,CH0,CA0 dihedral_coeff 21 fourier 1 0.0 1 2 # CA1,CA0,CH0,CA0 dihedral_coeff 22 fourier 1 3.625 -1 2 # CA0,TL@CS0,TL@CS0,CA0 dihedral_coeff 23 fourier 1 3.625 -1 2 # CS0,CS0,CA0,TL@CS0 dihedral_coeff 24 fourier 1 3.625 -1 2 # CS0,CS0,CA0,CL0 dihedral_coeff 25 fourier 1 3.625 -1 2 # OA0,CS0,CA0,TL@CS0 dihedral_coeff 26 fourier 1 3.625 -1 2 # OA0,CS0,CA0,CL0 dihedral_coeff 27 fourier 1 3.625 -1 2 # CA0,CS0,CS0,CA0 dihedral_coeff 28 fourier 1 3.625 -1 2 # CA0,CS0,CS0,OA0 dihedral_coeff 29 fourier 1 3.625 -1 2 # TL@CS0,TL@CS0,CA0,CS0 dihedral_coeff 30 fourier 1 3.625 -1 2 # TL@CS0,TL@CS0,CA0,CL0 dihedral_coeff 31 fourier 1 0.0 -1 2 # CS0,CA0,CL0,NL0 dihedral_coeff 32 fourier 1 0.0 -1 2 # TL@CS0,CA0,CL0,NL0 dihedral_coeff 33 fourier 1 0.9 -1 2 # CA0,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 # HL@OA0,CS0,CS0,CA1 dihedral_coeff 36 fourier 1 3.625 -1 2 # HL@OA0,CS0,CA1,CA0 dihedral_coeff 37 fourier 1 3.625 -1 2 # CS0,CS0,CA0,CS0 dihedral_coeff 38 fourier 1 3.625 -1 2 # OA0,CS0,CA0,CS0 improper_style none #Define kspace & rattale kspace_style pppm 0.00001 fix fRattleSPCE solvent rattle 0.0001 10 100 b 1 a 1 #Delete atoms if they overlap while merging delete_atoms overlap 2.0 solvent polymer mol yes #Define velocity & ensemble velocity all create 300.0 5463576 fix 1 all nvt temp 300.0 300.0 100.0 #timestep timestep 1.0 #Tracking the simulation thermo_style custom step temp press etotal density pe ke thermo 1000 dump d10 all custom 1000 water_nvt_*.cfg id type x y z #Run command run 50000 write_data merge.data