Monolayer protected Gold NP

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1

Hello everybody,
I need some help.
I’m having some problems simulating my Au79 nanoparticle coated with thiols in vacuum (for now).

When minimization begins, the gold core literally explode while thiols remain almost in their initial positions.

Here are the first section of the data.file and my input.

DATA.FILE:

"LAMMPS Description

401 atoms
331 bonds
536 angles
681 dihedrals
28 impropers

5 atom types
6 bond types
11 angle types
12 dihedral types
1 improper types

-50.0 50.0 xlo xhi
-50.0 50.0 ylo yhi
-50.0 50.0 zlo zhi

Pair Coeffs

1 5.29 2.951 #Au
2 1.85 0.12 #C
3 2.0 0.02 #H
4 1.60 0.20 #O
5 2.0 0.2 #S

Bond Coeffs

1 98.6 1.09 #C-H
2 553.0 0.96 #H-O
3 45.0 2.27 #Au-S
4 222.0 1.81 #C-S
5 260.0 1.526 #C-C
6 570.0 1.229 #C-O

Angle Coeffs

1 50.0 109.50 #H-C-S
2 35.0 109.0 #C-C-H
3 35.0 133.0 #C-O-H
4 88.0 110.0 #Au-S-Au
5 35.0 109.0 #H-C-H
6 180.0 349.0 #S-Au-S
7 90.0 110.0 #Au-S-C
8 50.0 114.7 #C-C-S
9 63.0 112.4 #C-C-C
10 80.0 126.0 #O-C-O
11 70.0 117.0 #C-C-O

Dihedral Coeffs

1 0.0 0.0 0.366 0.0 #C-C-C-H
2 0.0 0.0 0.452 0.0 #H-C-C-S
3 0.0 0.0 0.16 0.0 #H-C-S-Au
4 0.0 0.0 0.318 0.0 #H-C-C-H
5 0.0 0.0 0.16 0.0 #C-C-S-Au
6 0.0 0.0 0.0 0.0 #S-Au-S-C
7 1.711 -0.5 0.633 0.0 #C-C-C-O
8 0.0 4.83 0.0 0.0 #O-C-O-H
9 0.0 0.0 0.0 0.0 #S-Au-S-Au
10 1.876 0.0 0.0 0.0 #C-C-C-S
11 0.0 4.83 0.0 0.0 #C-C-O-H
12 0.0 0.0 0.0 0.0 #H-C-C-O

Improper Coeffs

1 10.5 180.0 #O-C-O-C

Masses

1 196.966553 # Au
2 12.010700 # C
3 1.007940 # H
4 15.999400 # O
5 32.064999 # S
"

INPUT:

"units real
dimension 3
atom_style full
region nano block -25 25 -25 25 -25 25 units box
boundary p p p

pair_style lj/cut 7.2
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style harmonic

read_data data.alkanethiolsnp

neighbor 0.3 bin
neigh_modify delay 5

#Minimization
reset_timestep 0
thermo 1
dump np all xyz 10 alkanethiolsnp.xyz
dump_modify np element Au C H O S
min_style sd
minimize 1.0e-7 1.0e-9 10000 10000

#Equilibration

reset_timestep 0
timestep 1
fix np all nvt temp 0.01 300 0.5
thermo 10

run 10000"

Thanks for your help.

Michele

2

Hello everybody,
I need some help.
I'm having some problems simulating my Au79 nanoparticle coated with thiols
in vacuum (for now).

When minimization begins, the gold core literally explode while thiols
remain almost in their initial positions.

that is likely due to bad parameters or bad initial coordinates.

Here are the first section of the data.file and my input.

this is useless. have you tried running the gold particle w/o the
thiols. or the thiols w/o the gold?

axel.

3

Great problem description. Sounds like your gold core is packed a
little tight. You may be able to get things to settle down by reining
in the minimizer initially:

min_modify dmax 0.0.001

If that does not work, you should seriously question the validity of
your structure and/or potential. A good sanity check is to dump the
forces for the initial structure.

4

Thanks for your answer Axel.
Initial coordinates and data.file were generated via TopoTools from an xyz file: the gold atoms were on lattice positions with a=4.08, while thiols were added manually with Gdis.

I tried to simulate only the gold core and what i got was that it was “breathing” around the equilibra positions.

The parameters in the data file were added manually from different articles and force fields. I assume they are expressed with right units.

Any suggestion?

Michele

5

For the MD part you may want to reduce the timestep. The oscillation frequency of your O-H and C-O

bonds is high (period about 8-9fs) thus the 1.0fs default timestep is a bit too large to properly integrate

those harmonic bonds (I tend to go with timestep ~ 1/20 of the oscillation period).

Carlos

6

Thanks Carlos, I’ll check that.

Anyway the problem is the core.
I assumed that there are only LJ interactions between gold atoms in the core, so the problem should be in LJ parameters in the data file.

One more question: is it normal that while minimizing, almost only gold atoms are moved from their initial position without moving sulfur and thiols chian bound to them?

Thanks

Michele

7

I set pair coeffs for Au-Au interaction as I set them in the only-gold simulation:

epsilon= 5.92
sigma= 2.951

but the results it’s really different from the first simulation.