MSD calculation

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1

Hi Lammps users,

Had taken a single organic molecule. Had converted the pdb file into .LAMPDAT file using OPEN BABEL.

Had used the following code.

LAMMPS data file generated by OpenBabel
26 atoms
26 bonds
42 angles
58 dihedrals
0 impropers
4 atom types
6 bond types
10 angle types
15 dihedral types
0 improper types
-5.40900 4.43900 xlo xhi
-5.40900 4.43900 ylo yhi
-5.40900 4.43900 zlo zhi

Masses

1 12.0107 # C
2 1.00794 # H
3 14.0067 # N
4 15.9994 # O

Atoms

1 1 1 0.00000 2.43400 -0.74400 -0.07300 # C
2 1 1 0.00000 2.13800 0.58400 0.25800 # C
3 1 4 -0.82000 3.10900 1.41100 0.74700 # O
4 1 2 0.41000 3.93900 0.91700 0.77900 # H
5 1 1 0.00000 0.84700 1.06700 0.08100 # C
6 1 2 0.41000 0.63900 2.10100 0.32200 # H
7 1 1 0.00000 -0.15800 0.23800 -0.42600 # C
8 1 1 0.00000 -1.57400 0.75400 -0.57100 # C
9 1 1 0.00000 -2.43000 0.50200 0.69500 # C
10 1 2 0.41000 -1.85600 0.83200 1.56500 # H
11 1 3 0.00000 -2.79700 -0.89800 0.85700 # N
12 1 2 0.41000 -2.82300 -1.14900 1.83600 # H
13 1 1 0.00000 -4.03500 -1.29000 0.19300 # C
14 1 2 0.41000 -4.90900 -0.68500 0.49100 # H
15 1 2 0.41000 -4.25000 -2.33800 0.41300 # H
16 1 2 0.41000 -3.92600 -1.20200 -0.89200 # H
17 1 2 0.41000 -3.32500 1.15000 0.63400 # H
18 1 4 -0.82000 -1.51200 2.15900 -0.84000 # O
19 1 2 0.41000 -2.40800 2.51000 -0.84000 # H
20 1 2 0.41000 -2.04600 0.23700 -1.41700 # H
21 1 1 0.00000 0.14900 -1.08100 -0.75800 # C
22 1 2 0.41000 -0.62100 -1.73600 -1.14800 # H
23 1 4 -0.82000 3.74300 -1.12800 0.13700 # O
24 1 2 0.41000 3.88000 -2.03000 -0.16700 # H
25 1 1 0.00000 1.44200 -1.57300 -0.57900 # C
26 1 2 0.41000 1.67800 -2.60100 -0.83900 # H

Bonds

1 2 10 11 # C: H
2 2 3 8 # C: H
3 2 23 26 # C: H
4 6 16 17 # O: H
5 5 16 10 # O: C
6 2 2 7 # C: H
7 1 3 2 # C: C
8 1 3 4 # C: C
9 1 2 1 # C: C
10 1 10 4 # C: C
11 1 10 18 # C: C
12 1 4 5 # C: C
13 6 14 15 # O: H
14 5 14 1 # O: C
15 1 1 6 # C: C
16 1 5 6 # C: C
17 2 5 9 # C: H
18 2 23 24 # C: H
19 2 23 25 # C: H
20 3 21 23 # N: C
21 5 12 6 # O: C
22 2 18 19 # C: H
23 3 21 18 # N: C
24 2 18 20 # C: H
25 6 12 13 # O: H
26 4 21 22 # N: H

Angles

1 9 14 1 2 # O: C: C
2 1 6 1 2 # C: C: C
3 9 14 1 6 # O: C: C
4 2 3 2 7 # C: C: H
5 2 1 2 7 # C: C: H
6 1 3 2 1 # C: C: C
7 2 2 3 8 # C: C: H
8 2 4 3 8 # C: C: H
9 1 4 3 2 # C: C: C
10 1 10 4 3 # C: C: C
11 1 5 4 3 # C: C: C
12 1 10 4 5 # C: C: C
13 1 6 5 4 # C: C: C
14 2 4 5 9 # C: C: H
15 2 6 5 9 # C: C: H
16 1 5 6 1 # C: C: C
17 9 12 6 1 # O: C: C
18 9 12 6 5 # O: C: C
19 10 16 10 11 # O: C: H
20 2 4 10 11 # C: C: H
21 2 18 10 11 # C: C: H
22 9 16 10 4 # O: C: C
23 9 16 10 18 # O: C: C
24 1 18 10 4 # C: C: C
25 5 6 12 13 # C: O: H
26 5 1 14 15 # C: O: H
27 5 10 16 17 # C: O: H
28 2 10 18 19 # C: C: H
29 7 21 18 10 # N: C: C
30 2 10 18 20 # C: C: H
31 8 21 18 19 # N: C: H
32 6 20 18 19 # H: C: H
33 8 21 18 20 # N: C: H
34 3 23 21 18 # C: N: C
35 4 23 21 22 # C: N: H
36 4 18 21 22 # C: N: H
37 6 26 23 24 # H: C: H
38 6 26 23 25 # H: C: H
39 8 21 23 26 # N: C: H
40 6 25 23 24 # H: C: H
41 8 21 23 24 # N: C: H
42 8 21 23 25 # N: C: H

Dihedrals

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

dimension 3
units metal
atom_style full
bond_style harmonic
dihedral_style none
boundary p p p
read_data INPUT.LMPDAT
pair_style lj/cut 1.25
pair_coeff * * 0.00650462 4
bond_coeff * 100.0 0.110
neighbor 0.4 bin
neigh_modify every 2 delay 10 check yes page 1000000
timestep 5.0
compute msd all msd average yes
fix msd all ave/time 1 1 1 c_msd[4] file msddumpfile
run 200

Have attached the graph (MSD Vs time). Is it correct?

Literature survey says that a straight line must be obtained. But the graph is not smooth. How to fix it?

Thanks,
Subashini.K

graph.JPG

2
3

Hello,

What sort of literature do you mean?Could you send your data points as a file please?

With best wishes
Anna

4

Hi Lammps users,

Had taken a single organic molecule. Had converted the pdb file into
.LAMPDAT file using OPEN BABEL.

Had used the following code.

[...]

dimension 3
units metal
atom_style full
bond_style harmonic
dihedral_style none
boundary p p p
read_data INPUT.LMPDAT
pair_style lj/cut 1.25
pair_coeff * * 0.00650462 4
bond_coeff * 100.0 0.110
neighbor 0.4 bin
neigh_modify every 2 delay 10 check yes page 1000000
timestep 5.0
compute msd all msd average yes
fix msd all ave/time 1 1 1 c_msd[4] file msddumpfile
run 200

Have attached the graph (MSD Vs time). Is it correct?

definitely NO. what you see is completely bogus.
there are *many* problems with your input. many pointing to conceptual
issues, i.e. you need proper tutoring in doing MD simulations.

- it doesn't make any sense *at all* to try and compute an MSD for a
single molecule, at least not without some kind of (implicit) solvent.
- your timestep of 5ps seconds is ridiculously large
- your lennard jones cutoff of 1.25 angstrom ridiculously short
- your bond length of 0.110 angstrom is extremely unusual of "a simple
organic molecule" and it is even more unusual that all bond would be
of the same length
- your simulation time of 500 steps without any indication of
equilibration is ludicrously short

Literature survey says that a straight line must be obtained. But the graph
is not smooth. How to fix it?

you need to learn a lot more about doing MD. talk to your adviser or
supervisor and find yourself a tutor and practice with a simpler
system, e.g. a liquid noble gas.

axel.