nanoparticles with a single grafted linear polymer

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1

Dear all

I’m trying to calculate spherical nanoparticles with a single grafted linear polymer.
Spherical nanoparticle diameter is treated as LJ spheres with diameter of 3.0 sigma.
Grafted polymer are treated as beads-spring of Kremer-Grest with standard parameters (bead diameter is set to 1.0 sigma and the number of bead per a chain is 10.).
I use langevin thermostat and nve. At first, to relax grafted polymers, I set LJ as purely repulsive interaction and run simulation. However, energy becomes huge and calculation stops very fast. And this warning displayed.

WARNING: FENE bond too long: 10904999 441 442 1.54137 (…/bond_fene.cpp:90)

Strangely, if in case that the number if grafted polymers is larger than 2, it work.

In only case of single grafted polymer system, this error occur.

In my data file, I define three types as follows;

type 1: bead of grafted polymer which grafted on the surface of nanoparticles.
type 2: nanoparticles
type 3: grafted polymers except type 1.

I treat type 1 and type 3 as rigid moleucle and exclude its interaction.

Here, I show my input file below.
///////////////////////////////////////////////////////////////////////////////////////////////

units lj
atom_style full
special_bonds fene

read_data PGNPs.np
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes page 100000

bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0

group PGNP type 1 2
group Chains type 3
neigh_modify exclude molecule PGNP

pair_style lj/cut 3.36
pair_modify shift yes
pair_coeff 1 1 0.0 1.0 1.12
pair_coeff 1 2 0.0 2.0 2.24
pair_coeff 1 3 0.0 1.0 1.12
pair_coeff 2 2 0.0 3.0 3.36
pair_coeff 2 3 0.0 2.0 2.24
pair_coeff 3 3 0.0 1.0 1.12

fix 1 Chains nve
fix 2 Chains langevin 1.0 1.0 1.0 904297
fix 3 PGNP rigid molecule langevin 1.0 1.0 1.0 904297
dump 1 all xyz 20000 dump_i.RC_Rod_AS5_AL03_N20_F1

thermo 20000
thermo_style custom step temp ke etotal press vol
timestep 0.005
restart 200000 restart_1i_temp restart_2i_temp
run 2000000
write_restart restart_i

///////////////////////////////////////////////////////////////////////////////////////////////

I am very confused. Please help me.

Best wishes,
Makoto

2

Dear all

I'm trying to calculate spherical nanoparticles with a single grafted linear
polymer.
Spherical nanoparticle diameter is treated as LJ spheres with diameter of
3.0 sigma.
Grafted polymer are treated as beads-spring of Kremer-Grest with standard
parameters (bead diameter is set to 1.0 sigma and the number of bead per a
chain is 10.).
I use langevin thermostat and nve. At first, to relax grafted polymers, I
set LJ as purely repulsive interaction and run simulation. However, energy
becomes huge and calculation stops very fast. And this warning displayed.

WARNING: FENE bond too long: 10904999 441 442 1.54137 (../bond_fene.cpp:90)

Strangely, if in case that the number if grafted polymers is larger than 2,
it work.
In only case of single grafted polymer system, this error occur.

In my data file, I define three types as follows;

type 1: bead of grafted polymer which grafted on the surface of
nanoparticles.
type 2: nanoparticles
type 3: grafted polymers except type 1.

I treat type 1 and type 3 as rigid moleucle and exclude its interaction.

Here, I show my input file below.
///////////////////////////////////////////////////////////////////////////////////////////////
units lj
atom_style full
special_bonds fene

read_data PGNPs.np
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes page 100000

bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0

group PGNP type 1 2
group Chains type 3
neigh_modify exclude molecule PGNP

pair_style lj/cut 3.36
pair_modify shift yes
pair_coeff 1 1 0.0 1.0 1.12
pair_coeff 1 2 0.0 2.0 2.24
pair_coeff 1 3 0.0 1.0 1.12
pair_coeff 2 2 0.0 3.0 3.36
pair_coeff 2 3 0.0 2.0 2.24
pair_coeff 3 3 0.0 1.0 1.12

all your LJ epsilon parameters are set to zero thus essentially
turning them off. how can this work? why even go through the effort of
defining different sigmas and cutoffs?

3

Dear Dr Alex

I’ve tried epsiron=1 for all pair, and the error occured as I mentioned. To understand the cause, I change parameters in pair coefficients and noticed that when epsiron is zero, meaning no interaction excep fene and repulsive LJ for neighbor beads, same error still occured. It’s very strange. As I mentioned, when the number of grafted polymers is larger than 2, no error happens. In other word, this error happens only in single grafted polymer system.

Makoto

4

Dear Dr Alex

I've tried epsiron=1 for all pair, and the error occured as I mentioned. To
understand the cause, I change parameters in pair coefficients and noticed
that when epsiron is zero, meaning no interaction excep fene and repulsive

when epsilon is zero there is *no* interaction. neither attraction,
nor repulsion.

LJ for neighbor beads, same error still occured. It's very strange. As I
mentioned, when the number of grafted polymers is larger than 2, no error
happens. In other word, this error happens only in single grafted polymer
system.

it is not that strange. most likely there is some problem with your
starting geometry.
also, i notice that for a simple bead-spring polymer, you should have
adjusted the special bond parameters, but i don't see that.

axel.

5

Dear Dr Axel

when epsilon is zero there is no interaction. neither attraction,
nor repulsion.

When epsilon is zero, there is no interaction except potential between connected beads defined by bond style ”fene”.

it is not that strange. most likely there is some problem with your
starting geometry.

I thought it, but still looking for the wrong things in data file.

also, i notice that for a simple bead-spring polymer, you should have
adjusted the special bond parameters, but i don’t see that.

Is it nessesary to adjust bond parameters to use simple beads spring model? I think I used standard parameters for KG model like spring coefficient=30, max lenght=1.5, epsilon for LJ=1.0. Why do I need to adjust them?

6

Dear Dr Axel

when epsilon is zero there is *no* interaction. neither attraction,
nor repulsion.

When epsilon is zero, there is no interaction except potential between
connected beads defined by bond style ”fene”.

it is not that strange. most likely there is some problem with your
starting geometry.

I thought it, but still looking for the wrong things in data file.

also, i notice that for a simple bead-spring polymer, you should have
adjusted the special bond parameters, but i don't see that.

Is it nessesary to adjust bond parameters to use simple beads spring model?
I think I used standard parameters for KG model like spring coefficient=30,
max lenght=1.5, epsilon for LJ=1.0. Why do I need to adjust them?

7

I think I have already used “special_bonds fene”.

Makoto