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Endo.in
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Endo.in
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# assign different molecular ID for each bead in one bead membrane, due to the commonad of compute chunk/atom
# assign the molecular ID of nanoparticle as the last one, for total area and volume computaiton because of the angle_rbc.cpp
units lj
dimension 3
atom_style hybrid ellipsoid molecular
boundary p p p
neighbor 1.0 bin
neigh_modify every 1 delay 1
#----------define the potential-------------------------------------------
dihedral_style bend
bond_style hybrid harmonic ljlr
angle_style rbc
pair_style hybrid fluidmembrane 2.6 lj42/cut 1.12246 lj/cosine1 1.1225 3.5
read_data R30_kb01_cubic.data
set type 1*2 shape 1 1 1
pair_coeff 1 1 fluidmembrane 1.0 1.0 2.6 4 3 0.0
pair_coeff 1 2 fluidmembrane 1.0 1.0 2.6 4 3 0.0
pair_coeff 2 2 fluidmembrane 1.0 1.0 2.6 4 3 0.0
pair_coeff 1*2 3*4 lj42/cut 1.0 1.12246 1.12246
pair_coeff 3*4 3*4 lj42/cut 1.0 1.12246 1.12246
pair_coeff 2 4 lj/cosine1 0.0 1.0 1.1225 15.5 # Ligand-Receptor
pair_modify pair lj42/cut shift yes
special_bonds lj 1.0 1.0 1.0 extra 100
comm_style tiled
comm_modify cutoff 6.0
group ND type 3 4
#initial velocities
group bilayer type 1 2
velocity bilayer create 0.18 492845 rot yes dist gaussian
velocity ND create 0.001 3333 rot yes dist gaussian
balance 1.1 rcb
fix fxbal all balance 10000 1.1 rcb
thermo 500
timestep 0.005
thermo_style custom step press ebond pxx pyy pzz lx ly lz
neigh_modify exclude molecule/intra ND
#--------------dump the bond position and velocity information---------------
dump 1 all custom 10000 smd.*.lammpstrj id mol type xu yu zu
dump_modify 1 sort id
compute 1 all property/local btype batom1 batom2
compute 2 all bond/local dist engpot force
dump 11 all local 10000 bond.*.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] c_2[3]
dump_modify 11 sort 1
group cbilayer type 1 2
compute corient cbilayer property/atom quatw quati quatj quatk
dump 2 all custom 10000 velocites.*.lammpstrj id vx vy vz c_corient[1] c_corient[2] c_corient[3] c_corient[4]
dump_modify 2 sort id
#--------------dump the bond position and velocity information---------------
#-----------ensemble for the bilayer and nanoparticle------------
group bilayer type 1 2
compute mytemp bilayer temp/asphere
compute mypress all pressure mytemp ke pair
fix fxnvt bilayer nvt/asphere temp 0.18 0.18 0.5
fix fxtens bilayer tension/berendsen1 x -0.07 -0.07 5 y -0.07 -0.07 5 couple xy modulus 18 dilate partial
fix_modify fxtens press mypress
#---------------------------------------------------------------
compute NDTemp ND temp
fix fixnve ND nve
fix fxlanND ND langevin 0.001 0.001 1 48279
fix_modify fxlanND temp NDTemp
#-----------ensemble for the bilayer and nanoparticle------------
#------------------out put the energy change during the endocytosis process --------------------------
group LP type 1 2
compute cpe12 LP pe/atom pair
compute rcpe12 LP reduce sum c_cpe12
compute rcpe13 LP group/group ND
fix fxoutlp all ave/time 1 100 1000 c_rcpe12 c_rcpe13 file potential_energy_LP.txt
compute cpe1 ND pe/atom bond
compute rcpe1 ND reduce sum c_cpe1
compute cpe2 ND pe/atom angle
compute rcpe2 ND reduce sum c_cpe2
compute cpe3 ND pe/atom dihedral
compute rcpe3 ND reduce sum c_cpe3
compute cpe4 ND pe/atom pair
compute rcpe4 ND reduce sum c_cpe4
fix fxoutnp all ave/time 1 100 1000 c_rcpe1 c_rcpe2 c_rcpe3 c_rcpe4 file potential_energy_NP.txt
#------------------out put the energy change during the endocytosis process --------------------------
fix n2 all bond/create 1 2 4 15.0 1 prob 1.0 85784 iparam 1 2 jparam 1 4
run 10
unfix n2
unfix fxnvt
unfix fxtens
uncompute mypress
uncompute mytemp
group bilayer delete
#------------------loop for the ligand-receptor interaction and receptor adding--------------------------
variable maxkeep equal 0
variable i loop 10000000
label loop1
group bilayer type 1 2
compute mytemp bilayer temp/asphere
compute mypress all pressure mytemp ke pair
fix fxnvt bilayer nvt/asphere temp 0.18 0.18 0.5
fix fxtens bilayer tension/berendsen1 x -0.07 -0.07 5 y -0.07 -0.07 5 couple xy modulus 18 dilate partial
fix_modify fxtens press mypress
group GLR type 2 4
compute NU GLR property/local btype
compute CNU GLR reduce sum c_NU
fix f2 GLR ave/time 1 1 100 c_CNU
fix n2 all bond/create 100 2 4 15.0 1 prob 1.0 8578 iparam 1 2 jparam 1 4
fix n3 all bond/break 100 1 15.1
thermo_style custom step temp etotal press lx ly lz f_n2[1] f_n2[2] f_n3[1] f_n3[2]
run 100
variable count1 equal f_f2
variable keep1 equal ${count1}
variable diff equal ${keep1}-${maxkeep}
print 'the difference between steps are ${diff}'
if "${count1}>${maxkeep}" then &
"variable maxkeep equal ${count1}"
variable xc1 equal xcm(ND,x)-lx/2
variable xc2 equal xcm(ND,x)+lx/2
variable yc1 equal xcm(ND,y)-ly/2
variable yc2 equal xcm(ND,y)+ly/2
change_box all x final ${xc1} ${xc2} y final ${yc1} ${yc2} units box
variable x1 equal xlo+6
variable x2 equal xhi-6
variable y1 equal ylo+6
variable y2 equal yhi-6
region regstrip1 block EDGE ${x1} EDGE EDGE EDGE EDGE side in units box
region regstrip2 block ${x2} EDGE EDGE EDGE EDGE EDGE side in units box
region regstrip3 block EDGE EDGE EDGE ${y1} EDGE EDGE side in units box
region regstrip4 block EDGE EDGE ${y2} EDGE EDGE EDGE side in units box
region regstrip union 4 regstrip1 regstrip2 regstrip3 regstrip4
if "${diff}>0" then &
"print 'the loop number for chaninge type is ${diff}' " &
"group liphead type 1 " &
"group regstrip region regstrip " &
"group lipbc intersect regstrip liphead " &
"variable orig equal count(lipbc) " &
"compute CCH lipbc chunk/atom molecule nchunk once ids once compress yes discard no" &
"run 0 post no" &
"dump CID lipbc custom 1 CID.*.dat id mol type c_CCH " &
"dump_modify CID sort id " &
"variable Judge equal ${diff}+1 " &
"variable Pmol atom 'c_CCH < v_Judge' " &
"group Tar dynamic lipbc var Pmol " &
"run 0 post no " &
"variable NTar equal count(Tar) " &
"print 'group Tar has ${NTar} atoms now' " &
"run 0 post no" &
"print 'group Tar has ${NTar} atoms now' " &
"group Tar static" &
"set group Tar type 2 " &
"group Tar delete " &
"uncompute CCH " &
"undump CID" &
"group lipbc delete" &
"group regstrip delete" &
"group liphead delete" &
"variable orig delete" &
"variable Judge delete" &
"variable Pmol delete" &
"variable NTar delete" &
unfix n2
unfix n3
region regstrip1 delete
region regstrip2 delete
region regstrip3 delete
region regstrip4 delete
region regstrip delete
variable count1 delete
variable keep1 delete
variable diff delete
variable xc1 delete
variable xc2 delete
variable yc1 delete
variable yc2 delete
variable x1 delete
variable x2 delete
variable y1 delete
variable y2 delete
uncompute mytemp
uncompute mypress
uncompute CNU
uncompute NU
unfix fxnvt
unfix fxtens
unfix f2
group bilayer delete
group GLR delete
next i
jump Endo.in loop1
write_data data.*