units real boundary p p p atom_style full neighbor 0.4 bin neigh_modify delay 2 every 1 kspace_style pppm 1.0e-4 bond_style harmonic angle_style charmm dihedral_style charmm pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic read_data cnt-gt1.data group cnt type 1 group gt1 type <> 2 32 group nagt1 type <> 2 33 group all type <> 1 33 pair_coeff 1 1 0.07 3.55 pair_coeff 2 2 0.046 0.4000135 pair_coeff 3 3 0.046 0.4000135 pair_coeff 4 4 0.046 1.959977 pair_coeff 5 5 0.046 0.4000135 pair_coeff 6 6 0.022 2.351973 pair_coeff 7 7 0.028 2.387609 pair_coeff 8 8 0.024 2.387609 pair_coeff 9 9 0.1 3.385415 pair_coeff 10 10 0.1 3.385415 pair_coeff 11 11 0.1 3.385415 pair_coeff 12 12 0.09 3.385415 pair_coeff 13 13 0.09 3.385415 pair_coeff 14 14 0.075 3.385415 pair_coeff 15 15 0.075 3.385415 pair_coeff 16 16 0.075 3.385415 pair_coeff 17 17 0.01 3.385415 pair_coeff 18 18 0.01 3.385415 pair_coeff 19 19 0.01 3.385415 pair_coeff 20 20 0.01 3.385415 pair_coeff 21 21 0.2 3.296325 pair_coeff 22 22 0.2 3.296325 pair_coeff 23 23 0.2 3.296325 pair_coeff 24 24 0.2 3.296325 pair_coeff 25 25 0.2 3.296325 pair_coeff 26 26 0.2 3.296325 pair_coeff 27 27 0.12 3.029056 pair_coeff 28 28 0.1521 3.153781 pair_coeff 29 29 0.12 3.029056 pair_coeff 30 30 0.1521 3.153781 pair_coeff 31 31 0.1521 3.153781 pair_coeff 32 32 0.585 3.830864 pair_coeff 33 33 0.0469 2.429926 neigh_modify exclude molecule cnt fix tocenter cnt recenter 0.0 0.0 0.0 units box unfix tocenter displace_atoms nagt1 move 0.0 7.0 0.0 units box fix freeze cnt setforce 0.0 0.0 0.0 velocity nagt1 create 300.0 4928459 dist gaussian fix 1 nagt1 nvt temp 300.0 300.0 100.0 timestep 0.5 #computes the ke and pe for all system #compute ke all ke #compute pe all pe compute temp gt1 temp #writes the information to a file for pe,ke, and temp fix energy gt1 ave/time 1 1 500 c_pe c_ke c_temp file energy.profile run 5000 dump 2 nagt1 atom 1000 cnt-gt1.dump dump 1 all xyz 1000 cnt-gt1.xyz run 15000