# 250 toluene system for drude polarizability example (Nose-Hoover) units real boundary p p p atom_style full bond_style harmonic angle_style harmonic dihedral_style opls improper_style opls special_bonds lj/coul 0.0 0.0 0.5 pair_style lj/cut/thole/long 2.600 8.0 8.0 pair_modify mix geometric tail yes kspace_style pppm 1.0e-4 read_data data.toluene extra/special/per/atom 1 comm_modify vel yes group gTOLUENE molecule 1:250 group gCORES type 1 2 3 4 5 6 7 group gDRUDES type 8 9 10 11 12 pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT neighbor 2.0 bin variable vTEMP equal 260.0 variable vTEMP_D equal 1.0 variable vPRESS equal 1.0 velocity gCORES create ${vTEMP} 12345 velocity gDRUDES create ${vTEMP_D} 12345 fix fDRUDE all drude C C C C C N N D D D D D fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 compute cTEMP_CORE gCORES temp/com compute cTEMP all temp/drude fix fDIRECT all drude/transform/direct fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 fix fINVERSE all drude/transform/inverse fix fMOMENTUM all momentum 100 linear 1 1 1 thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] thermo 50 timestep 0.5 run 2000