#thermalization of the Au - Bpdt system log log.run_au_bpdt_bcc_large_run14 units real boundary p p p atom_style full pair_style hybrid buck 14.0 lj/charmm/coul/long 14.0 16.0 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_neutr_15x18 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 thermo_style custom step temp epair emol etotal press c_Temp_layer & c_E_kin_layer thermo 100 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 200000 write_restart rst.au_bpdt_bcc_large_run14_heat unfix 2 unfix 3 fix 4 layer nvt 900 900 10 timestep 1 run 400000 write_restart rst.au_bpdt_bcc_large_run14_eq_nvt_hot unfix 4 fix 5 layer temp/berendsen 900 100 1 fix 6 layer nve fix_modify 5 temp Temp_layer timestep 1 run 1000000 write_restart rst.au_bpdt_bcc_large_run14_cool_100 unfix 5 unfix 6 unfix fdock ############################################################################### ############### 100K ########################################################## fix 7 layer nvt 100 100 10 fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nvt_100 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nvt_100 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nvt_100 id mol type x y z timestep 1 run 50000 write_restart rst.au_bpdt_bcc_large_run14_nvt_100 unfix 7 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom fix 8 layer nve fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nve_100 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nve_100 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nve_100 id mol type x y z timestep 1 run 100000 write_restart rst.au_bpdt_bcc_large_run14_nve_100 unfix 8 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom ############### heat to 150K ################################################### fix 9 layer temp/berendsen 100 150 1 fix 10 layer nve fix_modify 9 temp Temp_layer timestep 1 run 50000 write_restart rst.au_bpdt_bcc_large_run14_heat_150 unfix 9 unfix 10 #################### 150K ###################################################### fix 11 layer nvt 150 150 10 fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nvt_150 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nvt_150 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nvt_150 id mol type x y z timestep 1 run 50000 write_restart rst.au_bpdt_bcc_large_run14_nvt_150 unfix 11 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom fix 12 layer nve fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nve_150 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nve_150 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nve_150 id mol type x y z timestep 1 run 100000 write_restart rst.au_bpdt_bcc_large_run14_nve_150 unfix 12 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom ############### heat to 200K ################################################### fix 13 layer temp/berendsen 150 200 1 fix 14 layer nve fix_modify 13 temp Temp_layer timestep 1 run 50000 write_restart rst.au_bpdt_bcc_large_run14_heat_200 unfix 13 unfix 14 ###################### 200K #################################################### fix 15 layer nvt 200 200 10 fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nvt_200 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nvt_200 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nvt_200 id mol type x y z timestep 1 run 50000 write_restart rst.au_bpdt_bcc_large_run14_nvt_200 unfix 15 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom fix 16 layer nve fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nve_200 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nve_200 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nve_200 id mol type x y z timestep 1 run 100000 write_restart rst.au_bpdt_bcc_large_run14_nve_200 unfix 16 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom ############### heat to 300K ################################################### fix 17 layer temp/berendsen 200 300 1 fix 18 layer nve fix_modify 17 temp Temp_layer timestep 1 run 100000 write_restart rst.au_bpdt_bcc_large_run14_heat_300 unfix 17 unfix 18 ########################### 300K ################################################ fix 19 layer nvt 300 300 10 fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nvt_300 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nvt_300 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nvt_300 id mol type x y z timestep 1 run 50000 write_restart rst.au_bpdt_bcc_large_run14_nvt_300 unfix 19 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom fix 20 layer nve fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_au_bpdt_bcc_large14_eq_nve_300 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_bpdt_bcc_large14_eq_nve_300 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.au_bpdt_bcc_large14_eq_nve_300 id mol type x y z timestep 1 run 100000 write_restart rst.au_bpdt_bcc_large_run14_nve_300 unfix 20 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom