units lj atom_style hybrid sphere dipole molecular dimension 3 boundary p p p processors * * 1 # set the number of MPI processors in Lz direction to 1 read_data "polyspiral.in" #read_restart restart2.dat group mem type 1 # membrane beads group rest type 1 5 6 # non rigid particles group spiral type 2:4 # rigid polymer group receptor type 5 # membrane receptors group cargo type 6 # cargo particle set group all mass 1.0 # membrane parameters variable rc_global equal 2.6 variable rc equal 2.6 variable rmin equal 1.12 variable mu equal 3 variable zeta equal 4 variable eps equal 4.34 variable sigma equal 1.00 variable theta0_11 equal 0 # interaction parameters # membrane 1&5 with membrane spiral bead 4 (upper): variable sigma_spiral equal 1.00 variable sigma_mu equal (${sigma}+${sigma_spiral})/2 variable eps_mu equal 2 variable rc_mu equal (1.122462)*(${sigma_spiral}+${sigma})/2 # membrane 1&5 with membrane spiral bead 2,3 (inner, outer): variable sigma_spiral equal 1.00 variable sigma_ms equal (${sigma}+${sigma_spiral})/2 variable eps_ms equal 3 variable rc_ms equal (1.122462)*(${sigma_spiral}+${sigma})/2*1.3 # volume exclusion between spiral beads 2,3,4: variable eps_ss equal 2 variable sigma_ss equal ${sigma_spiral} variable rc_ss equal (1.122462)*${sigma_spiral} # membrane receptor 5 with cargo 6 variable sigma_cargo equal 16.00 variable sigma_rc equal (${sigma}+${sigma_cargo})/2 variable eps_rc equal 3 variable rc_rc equal (1.122462)*(${sigma_cargo}+${sigma})/2*1.5 # membrane receptor 1 & spiral beads 2/3/4 with cargo 6 variable sigma_mc equal (${sigma}+${sigma_cargo})/2 variable eps_mc equal 3 variable rc_mc equal (1.122462)*(${sigma_cargo}+${sigma})/2 bond_style harmonic bond_coeff 1 500 1.2794374289856747 #spiral1 bond_coeff 2 500 1.5468772665309858 #spiral1 bond_coeff 3 500 1.4700649617171933 #spiral1 bond_coeff 4 500 1.5468772665309858 #spiral1 bond_coeff 5 500 1.37 #spiral1 bond_coeff 6 500 1.5062398731346707 #spiral1 bond_coeff 7 500 1.4700649617171933 #spiral1 bond_coeff 8 500 1.5062398731346707 #spiral1 bond_coeff 9 500 1.1888748579713493 #spiral1 # Use hybrid overlay for pair_style membrane and lj/cut pair_style hybrid/overlay membrane ${rc_global} lj/cut ${rc_global} # pw359: Initialise LJ/expand to zero for all possible combinations pair_coeff * * lj/cut 0 0 # membrane attraction pair_coeff 1 2 lj/cut ${eps_ms} ${sigma_ms} ${rc_ms} pair_coeff 1 3 lj/cut ${eps_ms} ${sigma_ms} ${rc_ms} # volume exclusion membrane - spiral pair_coeff 1 4 lj/cut ${eps_mu} ${sigma_mu} ${rc_mu} # volume exclusion spiral - spiral pair_coeff 2 2 lj/cut ${eps_ss} ${sigma_ss} ${rc_ss} pair_coeff 2 3 lj/cut ${eps_ss} ${sigma_ss} ${rc_ss} pair_coeff 2 4 lj/cut ${eps_ss} ${sigma_ss} ${rc_ss} pair_coeff 3 3 lj/cut ${eps_ss} ${sigma_ss} ${rc_ss} pair_coeff 3 4 lj/cut ${eps_ss} ${sigma_ss} ${rc_ss} pair_coeff 4 4 lj/cut ${eps_ss} ${sigma_ss} ${rc_ss} #volume exclusion spiral&membrane - cargo pair_coeff 1 6 lj/cut ${eps_mc} ${sigma_mc} ${rc_mc} pair_coeff 2 6 lj/cut ${eps_mc} ${sigma_mc} ${rc_mc} pair_coeff 3 6 lj/cut ${eps_mc} ${sigma_mc} ${rc_mc} pair_coeff 4 6 lj/cut ${eps_mc} ${sigma_mc} ${rc_mc} # attraction receptor - cargo pair_coeff 5 6 lj/cut ${eps_rc} ${sigma_rc} ${rc_rc} # value exclusion receptor - spiral pair_coeff 2 5 lj/cut ${eps_ms} ${sigma_ms} ${rc_ms} pair_coeff 3 5 lj/cut ${eps_ms} ${sigma_ms} ${rc_ms} # attraction receptor - spiral pair_coeff 4 5 lj/cut ${eps_mu} ${sigma_mu} ${rc_mu} # same here for intra-membrane interactions pair_coeff 1 1 membrane ${eps} ${sigma} ${rmin} ${rc} ${zeta} ${mu} ${theta0_11} pair_coeff 1 5 membrane ${eps} ${sigma} ${rmin} ${rc} ${zeta} ${mu} ${theta0_11} pair_coeff 5 5 membrane ${eps} ${sigma} ${rmin} ${rc} ${zeta} ${mu} ${theta0_11} special_bonds lj 1 1 1 angle yes pair_modify shift yes # Reduce the delay from default 10 to 2 to get rid of dangeours builds #neigh_modify exclude molecule/intra spiral neigh_modify exclude molecule spiral neigh_modify delay 2 neigh_modify page 200000 one 20000 comm_modify cutoff 50 variable dofsub equal "count(mem)" compute cT all temp/sphere compute_modify cT extra ${dofsub} compute cKe all ke compute cPe all pe compute cErot all erotate/sphere variable E equal c_cKe+c_cPe+c_cErot variable K equal c_cKe variable P equal c_cPe variable Rot equal c_cErot compute emem all pair membrane compute elj all pair lj/cut ######################## INTEGRATORS ########################### fix fLANG all langevin 1.0 1.0 1 12341 zero yes omega yes fix fNPH rest nph/sphere x 0.0 0.0 10 y 0.0 0.0 10 & couple xy update dipole dilate all fix_modify fNPH temp cT press thermo_press fix filament spiral rigid/nve/small molecule dump coords all custom 1000 output.xyz id mol type x y z mux muy muz dump_modify coords sort id thermo_style custom step v_E v_P v_K v_Rot temp c_emem c_elj xhi yhi zhi restart 1000 restart1.dat restart2.dat # Equilibrate membrane timestep 0.01 thermo 1000 run 80000 # switch spiral to helix bond_style harmonic bond_coeff 1 500 1.1888748579713493 #helix bond_coeff 2 500 1.5062398731346707 #helix bond_coeff 3 500 1.4700649617171933 #helix bond_coeff 4 500 1.5062398731346707 #helix bond_coeff 5 500 1.37 #helix bond_coeff 6 500 1.5468772665309858 #helix bond_coeff 7 500 1.4700649617171933 #helix bond_coeff 8 500 1.5468772665309858 #helix bond_coeff 9 500 1.2794374289856747 #helix #unfix filament timestep 0.01 thermo 1000 run 100000 # switch helix to spiral bond_style harmonic bond_coeff 1 500 1.2794374289856747 #spiral3 bond_coeff 2 500 1.5468772665309858 #spiral3 bond_coeff 3 500 1.4700649617171933 #spiral3 bond_coeff 4 500 1.5468772665309858 #spiral3 bond_coeff 5 500 1.37 #spiral3 bond_coeff 6 500 1.5062398731346707 #spiral3 bond_coeff 7 500 1.4700649617171933 #spiral3 bond_coeff 8 500 1.5062398731346707 #spiral3 bond_coeff 9 500 1.1888748579713493 #spiral3 timestep 0.01 thermo 1000 run 300000 write_data "lastconfig.out" #end