Hello,
I am using LAMMPS 14 May 2016 version. My system has 6 chains, each having one atom type. So that makes it type 1 to 6. They are arranged in a bundle with an empty space between them. The bonds, angles, dihedrals are specified for the chains.
In the empty space between the chains, there are some atoms of type 7.
Interactions I want to specify are :
-
Beads of the same chain (types 1 to 1, 2 to 2, … and 6 to 6) - lj/cut wth cutoff 6 Ang
-
Beads of adjacent chains (types 1 to 2, 1 to 3 and so on…) - lj96/cut wth cutoff 5 Ang
-
Beads of non-bonded atoms in the empty space (types 7 to 7) - lj96/cut wth cutoff 9 Ang
-
Beads of type 7 and 1 to 6 - lj/cut
The pair coefficients of each case are different.
Now I am using pair style hybrid for this. I am specifying pair style hybrid like this: pair_style hybrid lj/cut 7.0 lj96/cut 9.0
Then the simulations are running but I am unsure of the accuracy.
When I am using this- pair_style hybrid lj/cut 7.0 lj96/cut 5.0 lj96/cut 9.0, I am getting an error saying : “ERROR: Expected integer parameter in input script or data file (…/pair_hybrid.cpp:386)”
Can anyone please help me with this?
I am attaching the input and date file below:
INPUT FILE
dimension 3
boundary p s p
units real
atom_style full
newton on
read_data data.model_water
neighbor 2.0 nsq
neigh_modify every 10 delay 10 check yes
echo both
group BottomChain_1 type 1
group MiddleChain_1 type 2
group TopChain_1 type 3
group BottomChain_2 type 4
group MiddleChain_2 type 5
group TopChain_2 type 6
group Water type 7
dump 1 all custom 1000 model_water.lammpstrj id type x y z
dump 2 BottomChain_1 custom 1000 BottomChain_1.lammpstrj id type x y z
dump 3 MiddleChain_1 custom 1000 MiddleChain_1.lammpstrj id type x y z
dump 4 TopChain_1 custom 1000 TopChain_1.lammpstrj id type x y z
dump 5 BottomChain_2 custom 1000 BottomChain_2.lammpstrj id type x y z
dump 6 MiddleChain_2 custom 1000 MiddleChain_2.lammpstrj id type x y z
dump 7 TopChain_2 custom 1000 TopChain_2.lammpstrj id type x y z
dump 8 Water custom 1000 Water.lammpstrj id type x y z
###SPECIFYING THE POTENTIAL
##NON BONDED POTENTIALS
pair_style hybrid lj/cut 7.0 lj96/cut 9.0
pair_modify shift yes
##BETWEEN BEADS IN A SINGLE CHAIN (INTRA)
pair_coeff 1 1 lj/cut 9.02 4.42
pair_coeff 2 2 lj/cut 9.02 4.42
pair_coeff 3 3 lj/cut 9.02 4.42
pair_coeff 4 4 lj/cut 9.02 4.42
pair_coeff 5 5 lj/cut 9.02 4.42
pair_coeff 6 6 lj/cut 9.02 4.42
##BETWEEN BEADS OF DIFFERENT CHAINS (INTER)
pair_coeff 1 26 lj96/cut 13.572 3.64
pair_coeff 2 36 lj96/cut 13.572 3.64
pair_coeff 3 46 lj96/cut 13.572 3.64
pair_coeff 4 56 lj96/cut 13.572 3.64
pair_coeff 5 6 lj96/cut 13.572 3.64
##BETWEEN BEADS IN WATER
pair_coeff 7 7 lj96/cut 0.821 2.918
##BETWEEN WATER BEADS AND CHAINS
pair_coeff 1*6 7 lj/cut 3.34 3.279
##BONDED POTENTIALS
bond_style harmonic
bond_coeff 1 90.283 5.64
angle_style harmonic
angle_coeff 1 366068.6906 163.272
dihedral_style harmonic
dihedral_coeff 1 8.409 1 1
special_bonds lj/coul 1.0 1.0 1.0
displace_atoms all random 0.01 0.01 0.01 443322
min_style cg
min_modify line quadratic
minimize 1.0e-20 1.0e-15 10000 1000000
thermo_style custom step cpu temp press vol pe ke ebond eangle edihed epair etotal
thermo 500
thermo_modify flush yes
timestep 0.5
fix 3 all nvt temp 300.0 300.0 10
run 100000
unfix 3
DATA FILE
LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Fri Dec 07 20:01:06 EST 2018
96 atoms
54 bonds
48 angles
42 dihedrals
0 impropers
7 atom types
1 bond types
1 angle types
1 dihedral types
0 improper types
-2.00000 53.500000 xlo xhi
-0.5000 8.100000 ylo yhi
-2.00000 6.200000 zlo zhi
Masses
1 162.1406 #
2 162.1406 #
3 162.1406 #
4 162.1406 #
5 162.1406 #
6 162.1406 #
7 18.01528 #
Atoms
1 1 1 0 0 0 0 #Chain1
2 2 1 0 5.64 0 0
3 3 1 0 11.28 0 0
4 4 1 0 16.9 0 0
5 5 1 0 22.559999 0 0
6 6 1 0 28.200001 0 0
7 7 1 0 33.84 0 0
8 8 1 0 39.48 0 0
9 9 1 0 45.119999 0 0
10 10 1 0 50.759998 0 0
11 11 2 0 0 3.64 0 #Chain2
12 12 2 0 5.64 3.64 0
13 13 2 0 11.28 3.64 0
14 14 2 0 16.9 3.64 0
15 15 2 0 22.559999 3.64 0
16 16 2 0 28.200001 3.64 0
17 17 2 0 33.84 3.64 0
18 18 2 0 39.48 3.64 0
19 19 2 0 45.119999 3.64 0
20 20 2 0 50.759998 3.64 0
21 21 3 0 0 7.28 0 #Chain3
22 22 3 0 5.64 7.28 0
23 23 3 0 11.28 7.28 0
24 24 3 0 16.9 7.28 0
25 25 3 0 22.559999 7.28 0
26 26 3 0 28.200001 7.28 0
27 27 3 0 33.84 7.28 0
28 28 3 0 39.48 7.28 0
29 29 3 0 45.119999 7.28 0
30 30 3 0 50.759998 7.28 0
31 31 5 0 0 3.64 3.64 #Chain5
32 32 5 0 5.64 3.64 3.64
33 33 5 0 11.28 3.64 3.64
34 34 5 0 16.9 3.64 3.64
35 35 5 0 22.559999 3.64 3.64
36 36 5 0 28.200001 3.64 3.64
37 37 5 0 33.84 3.64 3.64
38 38 5 0 39.48 3.64 3.64
39 39 5 0 45.119999 3.64 3.64
40 40 5 0 50.759998 3.64 3.64
41 41 4 0 0 0 3.64 #Chain4
42 42 4 0 5.64 0 3.64
43 43 4 0 11.28 0 3.64
44 44 4 0 16.9 0 3.64
45 45 4 0 22.559999 0 3.64
46 46 4 0 28.200001 0 3.64
47 47 4 0 33.84 0 3.64
48 48 4 0 39.48 0 3.64
49 49 4 0 45.119999 0 3.64
50 50 4 0 50.759998 0 3.64
51 51 6 0 0 7.28 3.64 #Chain6
52 52 6 0 5.64 7.28 3.64
53 53 6 0 11.28 7.28 3.64
54 54 6 0 16.9 7.28 3.64
55 55 6 0 22.559999 7.28 3.64
56 56 6 0 28.200001 7.28 3.64
57 57 6 0 33.84 7.28 3.64
58 58 6 0 39.48 7.28 3.64
59 59 6 0 45.119999 7.28 3.64
60 60 6 0 50.759998 7.28 3.64
61 61 7 0 25.38 3.64 1.82
62 62 7 0 23.88 3.64 1.82
63 63 7 0 26.88 3.64 1.82
64 64 7 0 22.38 3.64 1.82
65 65 7 0 28.38 3.64 1.82
66 66 7 0 20.88 3.64 1.82
67 67 7 0 29.88 3.64 1.82
68 68 7 0 25.38 2.00 1.82
69 69 7 0 23.88 2.00 1.82
70 70 7 0 26.88 2.00 1.82
71 71 7 0 22.38 2.00 1.82
72 72 7 0 28.38 2.00 1.82
73 73 7 0 20.88 2.00 1.82
74 74 7 0 29.88 2.00 0.5
75 75 7 0 25.38 2.00 0.5
76 76 7 0 23.88 2.00 0.5
77 77 7 0 26.88 2.00 0.5
78 78 7 0 22.38 2.00 0.5
79 79 7 0 28.38 2.00 0.5
80 80 7 0 10.38 1.5 0.79
81 81 7 0 11.38 1.5 0.79
82 82 7 0 12.38 1.5 0.79
83 83 7 0 13.38 1.5 0.79
84 84 7 0 14.38 1.5 0.79
85 85 7 0 15.38 1.5 0.79
86 86 7 0 16.38 1.5 0.79
87 87 7 0 32.38 3.64 1.82
88 88 7 0 33.88 3.64 1.82
89 89 7 0 35.38 3.64 1.82
90 90 7 0 36.88 3.64 1.82
91 91 7 0 38.38 3.64 1.82
92 92 7 0 39.88 3.64 1.82
93 93 7 0 41.38 3.64 1.82
94 94 7 0 42.88 1.64 1.82
95 95 7 0 44.38 2.64 1.82
96 96 7 0 46.38 2.00 1.00
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 1 11 12
11 1 12 13
12 1 13 14
13 1 14 15
14 1 15 16
15 1 16 17
16 1 17 18
17 1 18 19
18 1 19 20
19 1 21 22
20 1 22 23
21 1 23 24
22 1 24 25
23 1 25 26
24 1 26 27
25 1 27 28
26 1 28 29
27 1 29 30
28 1 31 32
29 1 32 33
30 1 33 34
31 1 34 35
32 1 35 36
33 1 36 37
34 1 37 38
35 1 38 39
36 1 39 40
37 1 41 42
38 1 42 43
39 1 43 44
40 1 44 45
41 1 45 46
42 1 46 47
43 1 47 48
44 1 48 49
45 1 49 50
46 1 51 52
47 1 52 53
48 1 53 54
49 1 54 55
50 1 55 56
51 1 56 57
52 1 57 58
53 1 58 59
54 1 59 60
Angles
1 1 1 2 3
2 1 2 3 4
3 1 3 4 5
4 1 4 5 6
5 1 5 6 7
6 1 6 7 8
7 1 7 8 9
8 1 8 9 10
9 1 11 12 13
10 1 12 13 14
11 1 13 14 15
12 1 14 15 16
13 1 15 16 17
14 1 16 17 18
15 1 17 18 19
16 1 18 19 20
17 1 21 22 23
18 1 22 23 24
19 1 23 24 25
20 1 24 25 26
21 1 25 26 27
22 1 26 27 28
23 1 27 28 29
24 1 28 29 30
25 1 31 32 33
26 1 32 33 34
27 1 33 34 35
28 1 34 35 36
29 1 35 36 37
30 1 36 37 38
31 1 37 38 39
32 1 38 39 40
33 1 41 42 43
34 1 42 43 44
35 1 43 44 45
36 1 44 45 46
37 1 45 46 47
38 1 46 47 48
39 1 47 48 49
40 1 48 49 50
41 1 51 52 53
42 1 52 53 54
43 1 53 54 55
44 1 54 55 56
45 1 55 56 57
46 1 56 57 58
47 1 57 58 59
48 1 58 59 60
Dihedrals
1 1 1 2 3 4
2 1 2 3 4 5
3 1 3 4 5 6
4 1 4 5 6 7
5 1 5 6 7 8
6 1 6 7 8 9
7 1 7 8 9 10
8 1 11 12 13 14
9 1 12 13 14 15
10 1 13 14 15 16
11 1 14 15 16 17
12 1 15 16 17 18
13 1 16 17 18 19
14 1 17 18 19 20
15 1 21 22 23 24
16 1 22 23 24 25
17 1 23 24 25 26
18 1 24 25 26 27
19 1 25 26 27 28
20 1 26 27 28 29
21 1 27 28 29 30
22 1 31 32 33 34
23 1 32 33 34 35
24 1 33 34 35 36
25 1 34 35 36 37
26 1 35 36 37 38
27 1 36 37 38 39
28 1 37 38 39 40
29 1 41 42 43 44
30 1 42 43 44 45
31 1 43 44 45 46
32 1 44 45 46 47
33 1 45 46 47 48
34 1 46 47 48 49
35 1 47 48 49 50
36 1 51 52 53 54
37 1 52 53 54 55
38 1 53 54 55 56
39 1 54 55 56 57
40 1 55 56 57 58
41 1 56 57 58 59
42 1 57 58 59 60