Hi all,
Im struggling with a little problem for weeks now and maybe you guys have some ideas.
Im tryin to align an amorphous polymer-network in such a way, that one of the terminal groups of my polymer-chains is as close as possible to the bottom of my simulation box (see appended png). The next step would be to add another polymer and link them. I didn’t expect the 1st step to be that hard and Im running out of ideas. The amorphous polymer was built using EMC.
I guess its not possible to get all the chain-ends to the bottom, but I would be happy if I could get just half of them down there (500 chains in total)
This is what I’ve tried so far:
units real
atom_style full
dimension 3
#newton on
boundary p p s
Style
pair_style lj/cut/coul/cut 12 9
bond_style harmonic
angle_style harmonic
dihedral_style multi/harmonic
improper_style harmonic
special_bonds lj/coul 0 0 0.5
pair_modify mix sixthpower
read_data retyped_unwrapped_newbox.data
include pa.params
Settings
dielectric 1.0
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
#timestep 0.5
timestep 2.0
dump d1 all custom 10000 align.*.atom id mol type q x y z
group linkers type 7
thermo_style custom step vol temp press density etotal pe ke c_radgyr
thermo 1000
variable low equal zlo
restart 25000 align.*.restart
fix 1 all nve
fix 2 all recenter NULL NULL INIT #if i dont use that, i will get a polymer-slurry at the bottom of my box
fix 3 all langevin 700.0 700.0 100.0 12345 #
#fix pull linkers spring tether 50.0 0 0 0 3.0 #
fix pull linkers drag NULL NULL ${low} 15.0 5.0 #pulling chain-terminators towards the bottom
#fix gyr all spring/rg 10.0 3000 # current:773.13038
run 5000000
Actually, it seems to work quite fine for a while. After some thousands of steps the dynamics slows down and i cant see any significant movement anymore. I was thinking about just displacing the chain-ends and minimze the structure afterwards. But i think this brute-force-method will result in a very unphysical structure.
Any hints?
regards,
frank.