#prime simulation settings units lj atom_style full boundary p p f #Simulation box description region simulation_box block 0 40 0 40 0 120 create_box 6 simulation_box bond/types 1 extra/bond/per/atom 2 extra/special/per/atom 5 #mass assignment mass * 1.0 #lattice definition lattice sc 1.0 #substrate insertion in the above mentioned box region xy block EDGE EDGE EDGE EDGE 0.0 1.0 side in units box create_atoms 1 region xy units box group substrate region xy set type 1 charge -0.1 fix 2 substrate setforce 0.0 0.0 0.0 #substrate insertion in the above mentioned box #region xyhi block EDGE EDGE EDGE EDGE 119.0 120.0 side in units box #create_atoms 1 region xyhi units box #group substrate2 region xyhi #fix 4 substrate2 setforce 0.0 0.0 0.0 fix wallhi all wall/lj93 zhi 119.0 1.5 1.0 2.5 units box fix_modify wallhi energy yes #polymer insertion in the above mentioned box molecule pe_positive pe_positive.tmp molecule counter_ion_positive counter-ion_positive.tmp molecule coion co-ion.tmp region simubox block EDGE EDGE EDGE EDGE 20.0 40.0 side in units box region box1 block EDGE EDGE EDGE EDGE 2 19.0 side in units box region box2 block EDGE EDGE EDGE EDGE 41.0 115.0 side in units box create_atoms 0 random 30 145678 simubox mol pe_positive 789145 units box create_atoms 0 random 900 568745 box1 mol counter_ion_positive 456879 units box create_atoms 0 random 320 458789 box2 mol coion 754214 units box group mobile type 2 3 4 #communication error #comm_modify mode single cutoff 10.0 vel yes #force field parameters #bond coefficient pair_style lj/cut/coul/long 2.5 10.0 pair_modify shift yes bond_style fene special_bonds fene bond_coeff * 30 1.5 1.0 1.0 kspace_style pppm 0.0001 kspace_modify slab 3.0 dielectric 1.0 #polymer and solvent-interaction pair coefficients definition pair_coeff 1 1 1.0 1.0 2.5 pair_coeff 1 2 1.0 1.0 2.5 pair_coeff 1 3 1.0 1.0 1.12 pair_coeff 1 4 1.0 1.0 1.12 pair_coeff 1 5 1.0 1.0 2.5 pair_coeff 1 6 1.0 1.0 1.12 pair_coeff 2 2 1.0 1.0 2.5 pair_coeff 2 3 1.0 1.0 1.12 pair_coeff 2 4 1.0 1.0 1.12 pair_coeff 2 5 1.0 1.0 2.5 pair_coeff 2 6 1.0 1.0 1.12 pair_coeff 3 3 1.0 1.0 1.12 pair_coeff 3 4 1.0 1.0 1.12 pair_coeff 3 5 1.0 1.0 2.5 pair_coeff 3 6 1.0 1.0 1.12 pair_coeff 4 4 1.0 1.0 1.12 pair_coeff 4 5 1.0 1.0 2.5 pair_coeff 4 6 1.0 1.0 1.12 pair_coeff 5 5 1.0 1.0 2.5 pair_coeff 5 6 1.0 1.0 1.12 pair_coeff 6 6 1.0 1.0 1.12 #Run settings timestep 0.005 run_style verlet neighbor 0.3 bin #neigh_modify one 10000 check yes once no cluster no binsize 10000 #minimization min_style cg minimize 1e-24 1e-24 50000 10000 #thermo_style custom step atoms temp epair etotal press #thermo 100 #thermo_modify temp add lost/bond ignore lost warn #thermo_style one #thermo_modify lost ignore #NVT fix fix 3 mobile nve fix 1 mobile langevin 1 1 2.0 48279 shell mkdir img_cdepo1 dump 1 all image 250000 img_cdepo1/*.jpg type type view 90 90 size 1000 1000 zoom 2 shell mkdir restart_cdepo1 #restart 50000 restart_cdepo1/poly.restart write_data after_min_40l.polymer thermo 100 run 10000 write_data 06_05_2022_40l.polymer #Deposition step 2 #polymer insertion in the above mentioned box molecule pe_negative pe_negative.tmp molecule counter_ion_negative counter-ion_negative.tmp create_atoms 0 random 30 789586 simubox mol pe_negative 458786 units box create_atoms 0 random 900 125478 box1 mol counter_ion_negative 145633 units box group mobile2 type 5 6 group between_sub union mobile mobile2 fix wallhi all wall/lj93 zhi 119.0 1.5 1.0 2.5 units box fix_modify wallhi energy yes shell mkdir img_cdepo2 dump 2 all image 250000 img_cdepo2/*.jpg type type view 90 90 size 1000 1000 zoom 2 shell mkdir restart_cdepo2 #restart 50000 restart_cdepo2/poly.restart #minimization min_style cg minimize 1e-24 1e-24 50000 10000 #NVT fix fix 4 between_sub nve fix 5 between_sub langevin 1.0 1.0 2.0 48279 write_data 06_05_2022_40l_aftermin_depo2.polymer thermo 100 run 10000 write_data 06_05_2022_40l_depo2.polymer