read_restart rst.au_bpdt_bcc_large_run14_cool_100 log log.restart_run14_heat_100 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 pair_coeff 1 * lj/charmm/coul/long 0.25 3.5635948725613571 pair_coeff 2 * lj/charmm/coul/long 0.086000000128358844 3.3996695079448309 pair_coeff 3 * lj/charmm/coul/long 0.015000000064220668 2.5996424587350853 pair_coeff 4 * lj/charmm/coul/long 0.015700000004219245 1.0690784617205229 pair_coeff 5 * lj/charmm/coul/long 0.25 3.5635948725613571 pair_coeff 6 * lj/charmm/coul/long 3 3 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 fix fshake layer shake 1e-4 20 0 t 3 4 unfix fdock ############################################################################### ############### 100K ########################################################## fix 7 layer nvt 100 100 10 fix s_coord dock coord/original fix msd_dock dock msd 1000 msd.dock_restart_large14_eq_nvt_100 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.au_restart_large14_eq_nvt_100 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.restart_large14_eq_nvt_100 id mol type x y z timestep 1 run 50000 write_restart rst.restart_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_restart_large14_eq_nve_100 compute sdpl dock displace/atom s_coord dump s dock custom 1000 sdpl.restart_large14_eq_nve_100 & c_sdpl[1] c_sdpl[2] c_sdpl[3] c_sdpl[4] dump catom layer_noh custom 1000 & layer.restart_large14_eq_nve_100 id mol type x y z timestep 1 run 100000 write_restart rst.resstart_large_run14_nve_100 unfix 8 unfix s_coord unfix msd_dock uncompute sdpl undump s undump catom