Prepare Polymer for End-Grafting

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.

step_2045000.PNG

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)

polymers are a big entangled mess. have you ever tried to pull a
single power cord out of a box of many of them, where the cables are
not rolled up in neat bundles?
i see two possible approaches:
1) consider the constraints of having endpoints are particular
locations already during the construction of the initial
configurations
2) start with soft-core non-bonded interactions and scale them down
so much, that molecules are easily move "through each other" and drag
your endpoints where you want them to be. follow this with gradually
restoring the full non-bonded interaction using fix adapt. see the
micelle input as simplified example for something like that.

axel.

I suggset you ask your Q to Pieter in’t Veld, the

author of EMC. He may have either MC or MD ideas

for you.

Steve

Thank you for ur suggestion. I’ve already tried to come into contact with him. He never replied…busy guy…I’ll try what Axel told me.

I suggset you ask your Q to Pieter in’t Veld, the

author of EMC. He may have either MC or MD ideas

for you.

Steve