#thermalization of the Au - Bpdt system log log.run_test11 units real boundary p p p atom_style full pair_style hybrid buck 14.0 lj/charmm/coul/long 14.0 16.0 pair_modify shift yes bond_style harmonic angle_style harmonic dihedral_style harmonic special_bonds amber kspace_style pppm 1.0e-4 lattice fcc 4.0782 orient x -1 -1 2 orient y 1 -1 0 orient z 1 1 1 & spacing 1 1 1 read_data data.layer_bpdt_bcc_neutr4x4 region au block INF INF INF INF -3.8 -0.5 create_atoms 6 region au pair_coeff 2 6 buck 10416.3 0.30 261.0 # C-Au pair_coeff 1 6 buck 1.5e6 0.22 6723.8 # S-Au pair_coeff 3 6 buck 6673.0 0.26 70.3 # H-Au pair_coeff 4 6 buck 6673.0 0.26 70.3 # H-Au pair_coeff 5 6 buck 1.5e6 0.22 6723.8 # S_dock-Au neighbor 2.0 bin neigh_modify every 1 delay 0 check yes exclude type 6 6 group metal type 6 group layer type 1 2 3 4 5 group dock type 5 group layer_noh type 1 2 5 velocity metal set 0 0 0 fix m metal setforce 0 0 0 velocity dock set 0 0 0 fix fdock dock setforce 0 0 0 compute Temp_layer layer temp compute E_kin_layer layer ke compute 1 all ke compute 2 all pe thermo_style custom step temp etotal c_Temp_layer & c_E_kin_layer pe ke thermo 10 minimize 1e-8 1e-8 1000 100000 fix fshake layer shake 1e-4 20 0 t 3 4 fix 2 layer temp/berendsen 0 900 1 fix 3 layer nve fix_modify 2 temp Temp_layer timestep 1 run 2000 unfix 2 unfix 3 write_restart rst.test11_heat fix 4 layer nvt 900 900 10 timestep 1 run 4000 unfix 4 write_restart rst.test11_nvt_hot fix 5 layer temp/berendsen 900 100 0.5 fix 6 layer nve fix_modify 5 temp Temp_layer timestep 1 run 2000 unfix 5 unfix 6 unfix fdock write_restart rst.test11_cool_100 ############################################################################### ############### 100K ########################################################## fix 7 layer nvt 100 100 10 fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_test11_nvt_100 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.test11_nvt_100 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.test11_nvt_100 id mol type x y z timestep 1 run 1500 unfix 7 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom