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[WIP] Workflow for ONA #28

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[WIP] Workflow for ONA #28

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7d89a16
added lammps_ona
zijiewu3 May 18, 2020
c1adf5c
Make minor edits and clear output
rmatsum836 May 18, 2020
e991475
changed notebook name
zijiewu3 May 19, 2020
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309 changes: 309 additions & 0 deletions lammps_ona/files/ONA.lammps
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files/ONA.lammps - created by mBuild; units = real

64 atoms
60 bonds
80 angles
28 dihedrals
0 impropers

8 atom types
6 bond types
8 angle types
4 dihedral types

0.000000 16.170000 xlo xhi
0.000000 10.880000 ylo yhi
0.000000 5.000001 zlo zhi

Masses

1 1.000000 # BBA
5 0.150000 # HBA
4 1.000000 # BBT
8 0.150000 # HBT
3 1.000000 # BBG
7 0.150000 # HBG
2 1.000000 # BBC
6 0.150000 # HBC

Pair Coeffs # lj
# epsilon (kcal/mol) sigma (Angstrom)
1 0.00000 0.00000 # BBA
5 0.00000 0.00000 # HBA
4 0.00000 0.00000 # BBT
8 0.00000 0.00000 # HBT
3 0.00000 0.00000 # BBG
7 0.00000 0.00000 # HBG
2 0.00000 0.00000 # BBC
6 0.00000 0.00000 # HBC

Bond Coeffs # harmonic
# k(kcal/mol/angstrom^2) req(angstrom)
1 1000.024 0.84 # BBA BBT
2 1000.024 0.37 # BBA HBA
3 1000.024 0.37 # BBC HBC
4 1000.024 0.84 # BBC BBG
5 1000.024 0.37 # BBT HBT
6 1000.024 0.37 # BBG HBG

Angle Coeffs # harmonic
# reduced_k theteq(deg)
1 299.999 180.00000 # BBC BBG BBC
2 2999.988 90.00000 # BBC BBG HBG
3 2999.988 90.00000 # BBG BBC HBC
4 299.999 180.00000 # BBT BBA BBT
5 299.999 180.00000 # BBG BBC BBG
6 2999.988 90.00000 # BBT BBA HBA
7 299.999 180.00000 # BBA BBT BBA
8 2999.988 90.00000 # BBA BBT HBT

Dihedral Coeffs # charmm
#k, n, phi, weight
1 6.00000 1 0 1.00000 # HBG BBG BBC HBC
2 3.00000 1 0 1.00000 # HBT BBT BBA HBA
3 6.00000 1 0 1.00000 # HBC BBC BBG HBG
4 3.00000 1 0 1.00000 # HBA BBA BBT HBT

Atoms

1 0 1 0.000000 -5.585000 2.940000 -0.000000
2 0 5 0.000000 -5.215000 2.940000 -0.000000
3 0 4 0.000000 -5.585000 2.100000 -0.000000
4 0 8 0.000000 -5.215000 2.100000 -0.000000
5 0 1 0.000000 -5.585000 1.260000 -0.000000
6 0 5 0.000000 -5.215000 1.260000 -0.000000
7 0 4 0.000000 -5.585000 0.420000 -0.000000
8 0 8 0.000000 -5.215000 0.420000 -0.000000
9 0 1 0.000000 -5.585000 -0.420000 -0.000000
10 0 5 0.000000 -5.215000 -0.420000 -0.000000
11 0 4 0.000000 -5.585000 -1.260000 0.000000
12 0 8 0.000000 -5.215000 -1.260000 0.000000
13 0 1 0.000000 -5.585000 -2.100000 0.000000
14 0 5 0.000000 -5.215000 -2.100000 0.000000
15 0 4 0.000000 -5.585000 -2.940000 0.000000
16 0 8 0.000000 -5.215000 -2.940000 0.000000
17 0 4 0.000000 -4.415000 2.940000 0.000000
18 0 8 0.000000 -4.785000 2.940000 -0.000000
19 0 1 0.000000 -4.415000 2.100000 0.000000
20 0 5 0.000000 -4.785000 2.100000 -0.000000
21 0 4 0.000000 -4.415000 1.260000 0.000000
22 0 8 0.000000 -4.785000 1.260000 -0.000000
23 0 1 0.000000 -4.415000 0.420000 0.000000
24 0 5 0.000000 -4.785000 0.420000 -0.000000
25 0 4 0.000000 -4.415000 -0.420000 0.000000
26 0 8 0.000000 -4.785000 -0.420000 -0.000000
27 0 1 0.000000 -4.415000 -1.260000 0.000000
28 0 5 0.000000 -4.785000 -1.260000 -0.000000
29 0 4 0.000000 -4.415000 -2.100000 0.000000
30 0 8 0.000000 -4.785000 -2.100000 -0.000000
31 0 1 0.000000 -4.415000 -2.940000 0.000000
32 0 5 0.000000 -4.785000 -2.940000 -0.000000
33 0 3 0.000000 4.415000 2.940000 -0.000000
34 0 7 0.000000 4.785000 2.940000 -0.000000
35 0 2 0.000000 4.415000 2.100000 -0.000000
36 0 6 0.000000 4.785000 2.100000 -0.000000
37 0 3 0.000000 4.415000 1.260000 -0.000000
38 0 7 0.000000 4.785000 1.260000 -0.000000
39 0 2 0.000000 4.415000 0.420000 -0.000000
40 0 6 0.000000 4.785000 0.420000 -0.000000
41 0 3 0.000000 4.415000 -0.420000 -0.000000
42 0 7 0.000000 4.785000 -0.420000 -0.000000
43 0 2 0.000000 4.415000 -1.260000 0.000000
44 0 6 0.000000 4.785000 -1.260000 0.000000
45 0 3 0.000000 4.415000 -2.100000 0.000000
46 0 7 0.000000 4.785000 -2.100000 0.000000
47 0 2 0.000000 4.415000 -2.940000 0.000000
48 0 6 0.000000 4.785000 -2.940000 0.000000
49 0 2 0.000000 5.585000 2.940000 0.000000
50 0 6 0.000000 5.215000 2.940000 -0.000000
51 0 3 0.000000 5.585000 2.100000 0.000000
52 0 7 0.000000 5.215000 2.100000 -0.000000
53 0 2 0.000000 5.585000 1.260000 0.000000
54 0 6 0.000000 5.215000 1.260000 -0.000000
55 0 3 0.000000 5.585000 0.420000 0.000000
56 0 7 0.000000 5.215000 0.420000 -0.000000
57 0 2 0.000000 5.585000 -0.420000 0.000000
58 0 6 0.000000 5.215000 -0.420000 -0.000000
59 0 3 0.000000 5.585000 -1.260000 0.000000
60 0 7 0.000000 5.215000 -1.260000 -0.000000
61 0 2 0.000000 5.585000 -2.100000 0.000000
62 0 6 0.000000 5.215000 -2.100000 -0.000000
63 0 3 0.000000 5.585000 -2.940000 0.000000
64 0 7 0.000000 5.215000 -2.940000 -0.000000

Bonds

1 2 2 1
2 1 3 1
3 1 3 5
4 5 3 4
5 2 6 5
6 1 7 9
7 1 7 5
8 5 8 7
9 2 9 10
10 5 11 12
11 1 11 9
12 1 11 13
13 1 13 15
14 2 14 13
15 5 16 15
16 1 17 19
17 5 17 18
18 2 20 19
19 1 21 23
20 5 21 22
21 1 21 19
22 1 23 25
23 2 23 24
24 1 25 27
25 5 25 26
26 2 27 28
27 1 27 29
28 5 30 29
29 1 31 29
30 2 31 32
31 6 34 33
32 4 35 37
33 3 35 36
34 4 35 33
35 4 37 39
36 6 38 37
37 4 39 41
38 3 40 39
39 6 42 41
40 3 43 44
41 4 43 45
42 4 43 41
43 6 45 46
44 4 45 47
45 3 48 47
46 3 49 50
47 4 49 51
48 6 51 52
49 4 51 53
50 3 54 53
51 4 55 57
52 6 55 56
53 4 55 53
54 3 58 57
55 4 59 57
56 6 59 60
57 4 59 61
58 3 62 61
59 4 63 61
60 6 64 63

Angles

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

Dihedrals

1 4 2 1 3 4
2 2 4 3 5 6
3 4 6 5 7 8
4 2 8 7 9 10
5 4 10 9 11 12
6 2 12 11 13 14
7 4 14 13 15 16
8 2 18 17 19 20
9 4 20 19 21 22
10 2 22 21 23 24
11 4 24 23 25 26
12 2 26 25 27 28
13 4 28 27 29 30
14 2 30 29 31 32
15 1 34 33 35 36
16 3 36 35 37 38
17 1 38 37 39 40
18 3 40 39 41 42
19 1 42 41 43 44
20 3 44 43 45 46
21 1 46 45 47 48
22 3 50 49 51 52
23 1 52 51 53 54
24 3 54 53 55 56
25 1 56 55 57 58
26 3 58 57 59 60
27 1 60 59 61 62
28 3 62 61 63 64
48 changes: 48 additions & 0 deletions lammps_ona/files/ONA.xml
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<ForceField>
<!-- Shown below are example entries for force field parameters.

Please refer to the OpenMM .xml specs for more info:
http://docs.openmm.org/7.0.0/userguide/application.html#writing-the-xml-file-->
<AtomTypes>
<Type name="BBA" class="BB" element="_BBA" mass="1" def="[_BBA]"/>
<Type name="BBC" class="BB" element="_BBC" mass="1" def="[_BBC]"/>
<Type name="BBG" class="BB" element="_BBG" mass="1" def="[_BBG]"/>
<Type name="BBT" class="BB" element="_BBT" mass="1" def="[_BBT]"/>
<Type name="HBA" class="HB" element="_HBA" mass="0.15" def="[_HBA]"/>
<Type name="HBC" class="HB" element="_HBC" mass="0.15" def="[_HBC]"/>
<Type name="HBG" class="HB" element="_HBG" mass="0.15" def="[_HBG]"/>
<Type name="HBT" class="HB" element="_HBT" mass="0.15" def="[_HBT]"/>
</AtomTypes>

<HarmonicBondForce>
<!-- Note: units of k are in eps/sigma^2-->
<Bond class1="BB" class2="BB" length="0.084" k="836820.083682"/>
<Bond class1="BB" class2="HB" length="0.037" k="836820.083682"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<!-- Note: units of k are in eps/rad^2-->
<Angle class1="BB" class2="BB" class3="BB" angle="3.1415926536" k="2510.39022621"/>
<Angle class1="HB" class2="BB" class3="BB" angle="1.57079632679" k="25103.9022621"/>
</HarmonicAngleForce>
<PeriodicTorsionForce>
<!-- Note, the units of k are in eps-->
<Proper type1="HBC" type2="BBC" type3="BBC" type4="HBC" periodicity1="1" phase1="0" k1="12.5523"/>
<Proper type1="HBC" type2="BBC" type3="BBT" type4="HBT" periodicity1="1" phase1="0" k1="12.5523"/>
<Proper type1="HBT" type2="BBT" type3="BBC" type4="HBC" periodicity1="1" phase1="0" k1="12.5523"/>
<Proper type1="HBT" type2="BBT" type3="BBT" type4="HBT" periodicity1="1" phase1="0" k1="12.5523"/>
<Proper type1="HBA" type2="BBA" type3="BBT" type4="HBT" periodicity1="1" phase1="0" k1="12.5523"/>
<Proper type1="HBT" type2="BBT" type3="BBA" type4="HBA" periodicity1="1" phase1="0" k1="12.5523"/>

<Proper type1="HBG" type2="BBG" type3="BBT" type4="HBT" periodicity1="1" phase1="0" k1="25.1046"/>
<Proper type1="HBT" type2="BBT" type3="BBG" type4="HBG" periodicity1="1" phase1="0" k1="25.1046"/>
<Proper type1="HBG" type2="BBG" type3="BBC" type4="HBC" periodicity1="1" phase1="0" k1="25.1046"/>
<Proper type1="HBC" type2="BBC" type3="BBG" type4="HBG" periodicity1="1" phase1="0" k1="25.1046"/>
<Proper type1="HBA" type2="BBA" type3="BBC" type4="HBC" periodicity1="1" phase1="0" k1="25.1046"/>
<Proper type1="HBC" type2="BBC" type3="BBA" type4="HBA" periodicity1="1" phase1="0" k1="25.1046"/>

<Proper type1="HBG" type2="BBG" type3="BBG" type4="HBG" periodicity1="1" phase1="0" k1="37.6569"/>
<Proper type1="HBA" type2="BBA" type3="BBA" type4="HBA" periodicity1="1" phase1="0" k1="37.6569"/>
<Proper type1="HBG" type2="BBG" type3="BBA" type4="HBA" periodicity1="1" phase1="0" k1="37.6569"/>
<Proper type1="HBA" type2="BBA" type3="BBG" type4="HBG" periodicity1="1" phase1="0" k1="37.6569"/>
</PeriodicTorsionForce>
</ForceField>
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