MD Simulation single polymer chain of polycarbonate using LAMMPS

LAMMPS LAMMPS Beginners
1

Dear Sir(s),
I want to do MD simulation of single polymer chain of polycarbonate, how to start to write input script and how to get the lammps data file to simulate in OVITO. Acutally i am working on to check the strain rate temperature depenedent damagae model for glassy amorphus polymer. Kindly help me with it.

I have generated Lammps data file for polycarbonate polymer chain using VMD and wrote some input script for the same:

LAMMPS data file generated by OpenBabel
35 atoms
36 bonds
59 angles
84 dihedrals
0 impropers
3 atom types
4 bond types
8 angle types
9 dihedral types
0 improper types
-2.67693 9.86557 xlo xhi
-2.67693 9.86557 ylo yhi
-2.67693 9.86557 zlo zhi

Masses

1 12.0107 # C
2 1.00794 # H
3 15.9994 # O

Atoms

1 1 1 0.00000 -1.06008 2.32079 -1.04896 # C
2 1 1 0.00000 -1.10367 1.23048 -0.19322 # C
3 1 1 0.00000 -0.08429 1.01074 0.72306 # C
4 1 2 0.41000 -0.10726 0.16293 1.39991 # H
5 1 1 0.00000 0.99250 1.90138 0.78037 # C
6 1 2 0.41000 1.77828 1.71903 1.51197 # H
7 1 1 0.00000 1.07725 3.01090 -0.08793 # C
8 1 1 0.00000 2.26998 3.99500 0.02409 # C
9 1 1 0.00000 1.97411 4.85669 1.27931 # C
10 1 2 0.41000 2.03593 4.26702 2.20210 # H
11 1 2 0.41000 2.67100 5.69719 1.37438 # H
12 1 2 0.41000 0.96649 5.28932 1.23609 # H
13 1 1 0.00000 3.64085 3.27300 0.09155 # C
14 1 1 0.00000 4.67704 3.71224 0.93825 # C
15 1 2 0.41000 4.54679 4.56836 1.59433 # H
16 1 1 0.00000 5.92178 3.07499 0.95506 # C
17 1 2 0.41000 6.69974 3.43676 1.62118 # H
18 1 1 0.00000 6.15316 1.99851 0.10564 # C
19 1 3 -0.82000 7.35908 1.28437 0.12426 # O
20 1 1 0.00000 8.52173 2.01534 -0.06366 # C
21 1 2 0.41000 9.36557 1.30938 -0.00157 # H
22 1 3 -0.82000 8.64261 3.21254 -0.26663 # O
23 1 1 0.00000 5.15023 1.53199 -0.73689 # C
24 1 2 0.41000 5.32655 0.67658 -1.38201 # H
25 1 1 0.00000 3.91104 2.17797 -0.75666 # C
26 1 2 0.41000 3.14789 1.81181 -1.44180 # H
27 1 1 0.00000 2.37682 4.96786 -1.17776 # C
28 1 2 0.41000 3.25975 5.61368 -1.09046 # H
29 1 2 0.41000 1.50762 5.63240 -1.24438 # H
30 1 2 0.41000 2.46192 4.43016 -2.13000 # H
31 1 3 -0.82000 -2.17693 0.39496 -0.28148 # O
32 1 2 0.41000 -2.07022 -0.31380 0.37352 # H
33 1 1 0.00000 0.02183 3.20493 -0.99769 # C
34 1 2 0.41000 0.00713 4.05032 -1.67951 # H
35 1 2 0.41000 -1.86896 2.48951 -1.75447 # H

Bonds

1 2 9 28 # C: H
2 2 1 20 # C: H
3 2 3 21 # C: H
4 2 14 32 # C: H
5 2 15 33 # C: H
6 2 9 27 # C: H
7 2 9 29 # C: H
8 1 9 7 # C: C
9 1 1 3 # C: C
10 1 1 2 # C: C
11 1 3 4 # C: C
12 1 14 15 # C: C
13 1 14 10 # C: C
14 1 15 13 # C: C
15 3 17 2 # O: C
16 4 17 35 # O: H
17 3 19 16 # O: C
18 1 2 6 # C: C
19 1 4 7 # C: C
20 1 4 5 # C: C
21 2 16 34 # C: H
22 3 18 16 # O: C
23 1 7 10 # C: C
24 1 7 8 # C: C
25 1 10 11 # C: C
26 3 18 13 # O: C
27 1 13 12 # C: C
28 1 6 5 # C: C
29 2 6 23 # C: H
30 2 5 22 # C: H
31 1 11 12 # C: C
32 2 11 30 # C: H
33 2 12 31 # C: H
34 2 8 25 # C: H
35 2 8 26 # C: H
36 2 8 24 # C: H

Angles

1 2 3 1 20 # C: C: H
2 2 2 1 20 # C: C: H
3 1 3 1 2 # C: C: C
4 6 17 2 1 # O: C: C
5 1 6 2 1 # C: C: C
6 6 17 2 6 # O: C: C
7 2 1 3 21 # C: C: H
8 2 4 3 21 # C: C: H
9 1 4 3 1 # C: C: C
10 1 7 4 3 # C: C: C
11 1 5 4 3 # C: C: C
12 1 7 4 5 # C: C: C
13 1 6 5 4 # C: C: C
14 2 4 5 22 # C: C: H
15 2 6 5 22 # C: C: H
16 1 5 6 2 # C: C: C
17 2 2 6 23 # C: C: H
18 2 5 6 23 # C: C: H
19 1 9 7 4 # C: C: C
20 1 10 7 9 # C: C: C
21 1 9 7 8 # C: C: C
22 1 10 7 4 # C: C: C
23 1 8 7 4 # C: C: C
24 1 10 7 8 # C: C: C
25 2 7 8 25 # C: C: H
26 2 7 8 26 # C: C: H
27 2 7 8 24 # C: C: H
28 5 26 8 25 # H: C: H
29 5 25 8 24 # H: C: H
30 5 26 8 24 # H: C: H
31 5 28 9 27 # H: C: H
32 5 29 9 28 # H: C: H
33 2 7 9 28 # C: C: H
34 5 29 9 27 # H: C: H
35 2 7 9 27 # C: C: H
36 2 7 9 29 # C: C: H
37 1 14 10 7 # C: C: C
38 1 14 10 11 # C: C: C
39 1 11 10 7 # C: C: C
40 1 12 11 10 # C: C: C
41 2 10 11 30 # C: C: H
42 2 12 11 30 # C: C: H
43 1 13 12 11 # C: C: C
44 2 13 12 31 # C: C: H
45 2 11 12 31 # C: C: H
46 6 18 13 15 # O: C: C
47 1 15 13 12 # C: C: C
48 6 18 13 12 # O: C: C
49 2 15 14 32 # C: C: H
50 2 10 14 32 # C: C: H
51 1 15 14 10 # C: C: C
52 2 14 15 33 # C: C: H
53 2 13 15 33 # C: C: H
54 1 14 15 13 # C: C: C
55 7 19 16 34 # O: C: H
56 8 19 16 18 # O: C: O
57 7 18 16 34 # O: C: H
58 4 2 17 35 # C: O: H
59 3 16 18 13 # C: O: C

Dihedrals

1 2 4 9 7 28 # C: C: C: H
2 2 10 9 7 28 # C: C: C: H
3 2 8 9 7 28 # C: C: C: H
4 2 4 9 7 27 # C: C: C: H
5 2 10 9 7 27 # C: C: C: H
6 2 8 9 7 27 # C: C: C: H
7 2 4 9 7 29 # C: C: C: H
8 2 10 9 7 29 # C: C: C: H
9 2 8 9 7 29 # C: C: C: H
10 6 21 1 3 20 # H: C: C: H
11 2 4 1 3 20 # C: C: C: H
12 2 2 1 3 21 # C: C: C: H
13 1 4 1 3 2 # C: C: C: C
14 8 17 1 2 20 # O: C: C: H
15 2 6 1 2 20 # C: C: C: H
16 7 17 1 2 3 # O: C: C: C
17 1 6 1 2 3 # C: C: C: C
18 2 7 3 4 21 # C: C: C: H
19 2 5 3 4 21 # C: C: C: H
20 1 7 3 4 1 # C: C: C: C
21 1 5 3 4 1 # C: C: C: C
22 6 33 14 15 32 # H: C: C: H
23 2 13 14 15 32 # C: C: C: H
24 2 10 14 15 33 # C: C: C: H
25 1 13 14 15 10 # C: C: C: C
26 2 7 14 10 32 # C: C: C: H
27 2 11 14 10 32 # C: C: C: H
28 1 7 14 10 15 # C: C: C: C
29 1 11 14 10 15 # C: C: C: C
30 8 18 15 13 33 # O: C: C: H
31 2 12 15 13 33 # C: C: C: H
32 7 18 15 13 14 # O: C: C: C
33 1 12 15 13 14 # C: C: C: C
34 5 1 17 2 35 # C: O: C: H
35 5 6 17 2 35 # C: O: C: H
36 1 5 2 6 1 # C: C: C: C
37 2 1 2 6 23 # C: C: C: H
38 7 17 2 6 5 # O: C: C: C
39 8 17 2 6 23 # O: C: C: H
40 1 9 4 7 3 # C: C: C: C
41 1 10 4 7 3 # C: C: C: C
42 1 8 4 7 3 # C: C: C: C
43 1 9 4 7 5 # C: C: C: C
44 1 10 4 7 5 # C: C: C: C
45 1 8 4 7 5 # C: C: C: C
46 1 6 4 5 3 # C: C: C: C
47 2 3 4 5 22 # C: C: C: H
48 1 6 4 5 7 # C: C: C: C
49 2 7 4 5 22 # C: C: C: H
50 9 19 16 18 13 # O: C: O: C
51 4 13 16 18 34 # C: C: O: H
52 1 14 7 10 9 # C: C: C: C
53 1 11 7 10 9 # C: C: C: C
54 1 14 7 10 4 # C: C: C: C
55 1 11 7 10 4 # C: C: C: C
56 1 14 7 10 8 # C: C: C: C
57 1 11 7 10 8 # C: C: C: C
58 2 9 7 8 25 # C: C: C: H
59 2 9 7 8 26 # C: C: C: H
60 2 9 7 8 24 # C: C: C: H
61 2 4 7 8 25 # C: C: C: H
62 2 4 7 8 26 # C: C: C: H
63 2 4 7 8 24 # C: C: C: H
64 2 10 7 8 25 # C: C: C: H
65 2 10 7 8 26 # C: C: C: H
66 2 10 7 8 24 # C: C: C: H
67 1 12 10 11 14 # C: C: C: C
68 2 14 10 11 30 # C: C: C: H
69 1 12 10 11 7 # C: C: C: C
70 2 7 10 11 30 # C: C: C: H
71 3 16 13 18 15 # C: C: O: C
72 3 16 13 18 12 # C: C: O: C
73 1 11 13 12 15 # C: C: C: C
74 2 15 13 12 31 # C: C: C: H
75 7 18 13 12 11 # O: C: C: C
76 8 18 13 12 31 # O: C: C: H
77 1 4 6 5 2 # C: C: C: C
78 2 2 6 5 22 # C: C: C: H
79 2 4 6 5 23 # C: C: C: H
80 6 22 6 5 23 # H: C: C: H
81 1 13 11 12 10 # C: C: C: C
82 2 10 11 12 31 # C: C: C: H
83 2 13 11 12 30 # C: C: C: H
84 6 31 11 12 30 # H: C: C: H

VARIABLES

variable fname index POLYCARBONATE.txt
variable simname index POLYCARBONATE

Initialization

units real
boundary p p p
atom_style molecular
log log.{simname}.txt read_data {fname}0

Dreiding potential information

neighbor 0.4 bin
neigh_modify every 10 one 10000
bond_style harmonic
bond_coeff 1 350 1.53
angle_style harmonic
angle_coeff 1 60 109.5
dihedral_style multi/harmonic
dihedral_coeff 1 1.73 -4.49 0.776 6.99 0.0
pair_style lj/cut 10.5
pair_coeff 1 1 0.112 4.01 10.5

compute csym all centro/atom fcc
compute peratom all pe/atom

#####################################################

Equilibration (Langevin dynamics at 5000 K)

velocity all create 5000.0 1231
fix 1 all nve/limit 0.05
fix 2 all langevin 5000.0 5000.0 10.0 904297
thermo_style custom step temp
thermo 10000
timestep 1
run 1000000
unfix 1
unfix 2
write_restart restart.${simname}.dreiding1

#####################################################

Define Settings

compute eng all pe/atom
compute eatoms all reduce sum c_eng

#####################################################

Minimization

dump 1 all cfg 6 dump.comp_*.cfg mass type xs ys zs c_csym c_peratom fx fy fz

reset_timestep 0
fix 1 all nvt temp 500.0 500.0 100.0
thermo 20
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
min_style cg
minimize 1e-25 1e-25 500000 1000000

print “All done”

*Kindly check my input script

2

*Kindly check the forum rules

Your post contains no question, we don’t know what you want to achieve with the simulation, and you are referring to ovito, VMD, open babel, LAMMPS…

Simon

3

I am working on the development of rate and temperature dependent damage model for glassy amorphous polymers. How to write an input script for a single polymer chain of polycarbonate for MD Simulation in Lammps?

Pls help

4

Not like this. First you have to learn about and understand how force fields work and how force field types are assigned to atoms, bonds, angles, dihedrals, and impropers for your force field of choice. I would also expect that you need to assign partial charges to atoms and for that there is either an increment based rule after how you can determine those or you need a database of molecule fragments (i.e. like residues representing individual amino acids in a protein) where the charge distribution for your specific fragments are determined. The force field then also determines which pair styles and other styles you will need to define to apply those force field parameters. None of the programs you have been using has any knowledge of that and thus this cannot be done automatically.

As the saying goes, “there ain’t no escape from the blues”. Or said differently, you have to know and learn what you are doing and nobody will take the burden of doing that from you since you cannot do meaningful simulations without it.

Please have the courtesy and spell out words. There is no character limit on messages here.