1 |
< |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF). |
2 |
< |
// |
3 |
< |
// The sections are divided into AtomTypes, BondTypes, BendTypes, |
4 |
< |
// and TorsionTypes. |
5 |
< |
// |
6 |
< |
// Many parameters (but not all) are derived from the TRAPPE force field |
7 |
< |
// of Siepmann's group. |
8 |
< |
|
9 |
< |
begin AtomTypes |
10 |
< |
//Atom isDipole isSSD mass LJ epsilon ( kcal/mol) LJ sigma (Angstroms) Dipole Moment (Debye) w0 v0 (kcal/mol) v0p (kcal/mol) rl (Angstroms) ru (Angstroms) rlp (Angstroms) rup (Angstroms) |
11 |
< |
|
12 |
< |
CH4 0 0 16.05 0.279 3.73 |
13 |
< |
CH3 0 0 15.04 0.185 3.75 |
14 |
< |
CH2 0 0 14.03 0.0866 3.95 |
15 |
< |
CH 0 0 13.02 0.0189 4.68 |
16 |
< |
SSD 1 1 18.0153 0.152 3.035 2.42 0.07715 3.9 3.9 2.4 3.8 2.75 3.35 |
17 |
< |
HEAD 1 0 196 0.185 5.75 20.6 |
18 |
< |
TB1 0 0 14.03 0.0866 4.0 |
19 |
< |
TE1 0 0 15.04 0.185 4.0 |
20 |
< |
TB2 0 0 21.05 0.25 6.0 |
21 |
< |
TE2 0 0 22.56 0.5 6.0 |
22 |
< |
TB3 0 0 28.06 0.5 8.0 |
23 |
< |
TE3 0 0 30.08 0.75 8.0 |
24 |
< |
|
25 |
< |
end AtomTypes |
26 |
< |
|
27 |
< |
begin BondTypes |
28 |
< |
|
29 |
< |
//Atom1 Atom2 FixedBondType |
30 |
< |
//V_FixedBondType = 0 |
31 |
< |
|
32 |
< |
//Atom1 Atom2 HarmonicBondType b0 Kb (kcal/mol) |
33 |
< |
//V_HarmonicBondType = Kb(b- bo)^2 |
34 |
< |
//HarmonicBondType Examples |
35 |
< |
HEAD CH3 HarmonicBondType 2.75 260 |
36 |
< |
HEAD CH2 HarmonicBondType 2.75 260 |
37 |
< |
HEAD CH HarmonicBondType 2.75 260 |
38 |
< |
HEAD TB1 HarmonicBondType 2.76 260 |
39 |
< |
HEAD TB2 HarmonicBondType 3.20 260 |
40 |
< |
HEAD TB3 HarmonicBondType 3.63 260 |
41 |
< |
CH3 CH3 HarmonicBondType 1.526 260 |
42 |
< |
CH3 CH2 HarmonicBondType 1.526 260 |
43 |
< |
CH3 CH HarmonicBondType 1.526 260 |
44 |
< |
CH2 CH2 HarmonicBondType 1.526 260 |
45 |
< |
CH2 CH HarmonicBondType 1.526 260 |
46 |
< |
CH CH HarmonicBondType 1.526 260 |
47 |
< |
TB1 TB1 HarmonicBondType 1.526 260 |
48 |
< |
TB2 TB2 HarmonicBondType 2.34 260 |
49 |
< |
TB3 TB3 HarmonicBondType 3.12 260 |
50 |
< |
TB1 TE1 HarmonicBondType 1.526 260 |
51 |
< |
TB2 TE2 HarmonicBondType 2.34 260 |
52 |
< |
TB3 TE3 HarmonicBondType 3.12 260 |
53 |
< |
|
54 |
< |
//Atom1 Atom2 CubicBondType b0 K3 K2 K1 K0 |
55 |
< |
//V_CubicBondType = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
56 |
< |
|
57 |
< |
|
58 |
< |
//Atom1 Atom2 QuadraticBondType b0 K4 K3 K2 K1 K0 |
59 |
< |
//V_QuadraticBondType = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
60 |
< |
|
61 |
< |
|
62 |
< |
//Atom1 Atom2 PolynomialBondType b0 i Ki [j Kj] |
63 |
< |
//V_QuadraticBondType = Ki(b - b0)^i + Kj(b - b0)^j + ... |
64 |
< |
|
65 |
< |
|
66 |
< |
end BondTypes |
67 |
< |
|
68 |
< |
begin BendTypes |
69 |
< |
|
70 |
< |
//HarmonicBendType |
71 |
< |
//Atom1 Atom2 Atom3 HarmonicBendType Ktheta Theta0 |
72 |
< |
//V_HarmonicBendType = Ktheta(Theta - Theta0)^2 |
73 |
< |
//Ktheta: kcal/mole/rad**2 |
74 |
< |
//Theta0: degrees |
75 |
< |
//HarmonicBendType examples |
76 |
< |
HEAD CH2 HEAD HarmonicBendType 58.84 114.0 |
77 |
< |
HEAD CH2 CH3 HarmonicBendType 58.84 114.0 |
78 |
< |
HEAD CH2 CH2 HarmonicBendType 58.84 114.0 |
79 |
< |
HEAD TB1 TB1 HarmonicBendType 58.84 114.0 |
80 |
< |
HEAD TB2 TB2 HarmonicBendType 58.84 114.0 |
81 |
< |
HEAD TB3 TB3 HarmonicBendType 58.84 114.0 |
82 |
< |
HEAD CH2 CH HarmonicBendType 58.84 114.0 |
83 |
< |
HEAD CH CH3 HarmonicBendType 58.84 112.0 |
84 |
< |
HEAD CH CH2 HarmonicBendType 58.84 112.0 |
85 |
< |
HEAD CH CH HarmonicBendType 58.84 112.0 |
86 |
< |
CH3 CH2 CH3 HarmonicBendType 58.84 114.0 |
87 |
< |
CH3 CH2 CH2 HarmonicBendType 58.84 114.0 |
88 |
< |
CH3 CH2 CH HarmonicBendType 58.84 114.0 |
89 |
< |
CH3 CH CH3 HarmonicBendType 58.84 112.0 |
90 |
< |
CH3 CH CH2 HarmonicBendType 58.84 112.0 |
91 |
< |
CH3 CH CH HarmonicBendType 58.84 112.0 |
92 |
< |
CH2 CH2 CH2 HarmonicBendType 58.84 114.0 |
93 |
< |
CH2 CH2 CH HarmonicBendType 58.84 114.0 |
94 |
< |
CH2 CH CH2 HarmonicBendType 58.84 112.0 |
95 |
< |
CH2 CH CH HarmonicBendType 58.84 112.0 |
96 |
< |
CH CH2 CH HarmonicBendType 58.84 114.0 |
97 |
< |
CH CH CH HarmonicBendType 58.84 112.0 |
98 |
< |
TB1 TB1 TB1 HarmonicBendType 58.84 114.0 |
99 |
< |
TB2 TB2 TB2 HarmonicBendType 58.84 114.0 |
100 |
< |
TB3 TB3 TB3 HarmonicBendType 58.84 114.0 |
101 |
< |
TE1 TB1 TB1 HarmonicBendType 58.84 114.0 |
102 |
< |
TE2 TB2 TB2 HarmonicBendType 58.84 114.0 |
103 |
< |
TE3 TB3 TB3 HarmonicBendType 58.84 114.0 |
104 |
< |
|
105 |
< |
//GhostBend |
106 |
< |
//Atom1 Atom2 GHOST GhostBendType Ktheta Theta0 |
107 |
< |
//Atom2 must be directional atom |
108 |
< |
//GhostBendType examples |
109 |
< |
CH2 HEAD GHOST GhostBendType 0.00176972 129.783 |
110 |
< |
CH2 HEAD GHOST GhostBendType 58.84 90.0 |
111 |
< |
TB1 HEAD GHOST GhostBendType 58.84 90.0 |
112 |
< |
TB2 HEAD GHOST GhostBendType 58.84 90.0 |
113 |
< |
TB3 HEAD GHOST GhostBendType 58.84 90.0 |
114 |
< |
|
115 |
< |
//UreyBradleyBend |
116 |
< |
//Atom1 Atom2 Atom3 UreyBradleyBend Ktheta Theta0 Kub S0 |
117 |
< |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
118 |
< |
//Ktheta: kcal/mole/rad**2 |
119 |
< |
//Theta0: degrees |
120 |
< |
//Kub: kcal/mole/A**2 |
121 |
< |
//S0: A |
122 |
< |
|
123 |
< |
//CubicBendType |
124 |
< |
//Atom1 Atom2 Atom3 CubicBendType Theta0 K3 K2 K1 K0 |
125 |
< |
//V_CubicBendType = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
126 |
< |
|
127 |
< |
//QuadraticBendType |
128 |
< |
//Atom1 Atom2 Atom3 QuadraticBendType Theta0 K4 K3 K2 K1 K0 |
129 |
< |
//V_QuadraticBendType = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
130 |
< |
|
131 |
< |
//PolynomialBendType |
132 |
< |
//Atom1 Atom2 Atom3 PolynomialBendType Theta0 i Ki [j Kj] |
133 |
< |
//V_PolynomialBendType = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
134 |
< |
|
135 |
< |
end BendTypes |
136 |
< |
|
137 |
< |
begin TorsionTypes |
138 |
< |
|
139 |
< |
//CubicTorsionType |
140 |
< |
//Atom1 Atom2 Atom3 Atom4 CubicTorsionType k3 k2 k1 k0 ( all are kcal/mol ) |
141 |
< |
//V_CubicTorsionType = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
142 |
< |
//CubicTorsionType Examples |
143 |
< |
HEAD CH2 CH2 HEAD CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
144 |
< |
HEAD CH2 CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
145 |
< |
HEAD CH CH HEAD CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
146 |
< |
HEAD CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
147 |
< |
HEAD CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
148 |
< |
HEAD CH CH2 CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
149 |
< |
HEAD CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
150 |
< |
HEAD CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
151 |
< |
HEAD CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
152 |
< |
HEAD CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
153 |
< |
HEAD CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
154 |
< |
HEAD CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
155 |
< |
HEAD CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
156 |
< |
HEAD CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
157 |
< |
HEAD CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
158 |
< |
HEAD TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
159 |
< |
HEAD TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
160 |
< |
HEAD TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
161 |
< |
CH3 CH2 CH2 CH3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
162 |
< |
CH3 CH2 CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
163 |
< |
CH3 CH CH CH3 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
164 |
< |
CH3 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
165 |
< |
CH3 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
166 |
< |
CH3 CH CH2 CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
167 |
< |
CH3 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
168 |
< |
CH3 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
169 |
< |
CH3 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
170 |
< |
CH3 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
171 |
< |
CH3 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
172 |
< |
CH2 CH2 CH2 CH2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
173 |
< |
CH2 CH2 CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
174 |
< |
CH2 CH CH CH2 CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
175 |
< |
CH2 CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
176 |
< |
CH2 CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
177 |
< |
CH2 CH CH2 CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
178 |
< |
CH2 CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
179 |
< |
CH CH2 CH2 CH CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
180 |
< |
CH CH2 CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
181 |
< |
CH CH CH CH CubicTorsionType 3.3254 -0.4215 -1.686 1.1661 |
182 |
< |
TB1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
183 |
< |
TB2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
184 |
< |
TB3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
185 |
< |
TE1 TB1 TB1 TB1 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
186 |
< |
TE2 TB2 TB2 TB2 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
187 |
< |
TE3 TB3 TB3 TB3 CubicTorsionType 5.9602 -0.2568 -3.802 2.1586 |
188 |
< |
|
189 |
< |
//CharmmTorsionType |
190 |
< |
//Atom1 Atom2 Atom3 Atom4 CharmmTorsionType Kchi n delta [Kchi n delta] |
191 |
< |
//V_CharmmTorsionType = Kchi(1 + cos(n(chi) - delta)) |
192 |
< |
//Kchi: kcal/mole |
193 |
< |
//n: multiplicity |
194 |
< |
//delta: degrees |
195 |
< |
//in some cases, a CharmmTorsionType may have two or three terms. If n is equal to 0, it falls back to harmonic form |
196 |
< |
|
197 |
< |
//QuadraticTorsionType |
198 |
< |
//Atom1 Atom2 Atom3 Atom4 QuadraticTorsionType k4 k3 k2 k1 k0 ( all are kcal/mol ) |
199 |
< |
//V_QuadraticTorsionType = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
200 |
< |
|
201 |
< |
//PolynomialTorsionType |
202 |
< |
//Atom1 Atom2 Atom3 Atom4 PolynomialTorsionType i Ki [j Kj] |
203 |
< |
//VPolynomialTorsionType = Ki (cos phi)^i + ... + Kj (cos phi)^j |
204 |
< |
|
205 |
< |
end TorsionTypes |
1 |
> |
// This is the forcefield file for the Dipolar Unified-atom Force Field (DUFF) |
2 |
> |
// |
3 |
> |
// The sections are divided into AtomTypes |
4 |
> |
// |
5 |
> |
//any parameters (but not all) are derived from the TRAPPE force field |
6 |
> |
// of Siepmann's group. |
7 |
> |
begin AtomTypes |
8 |
> |
//Name mass (amu) |
9 |
> |
CH4 16.05 |
10 |
> |
CH3 15.04 |
11 |
> |
CH2 14.03 |
12 |
> |
CH 13.02 |
13 |
> |
SSD 18.0153 |
14 |
> |
SSD1 18.0153 |
15 |
> |
SSD_E 18.0153 |
16 |
> |
SSD_RF 18.0153 |
17 |
> |
HEAD 196 |
18 |
> |
TB1 14.03 |
19 |
> |
TE1 15.04 |
20 |
> |
TB2 21.05 |
21 |
> |
TE2 22.56 |
22 |
> |
TB3 28.06 |
23 |
> |
TE3 30.08 |
24 |
> |
H 1.00794 |
25 |
> |
He 4.002602 |
26 |
> |
C 12.0107 |
27 |
> |
N 14.00674 |
28 |
> |
O 15.9994 |
29 |
> |
F 18.9984032 |
30 |
> |
Ne 20.1797 |
31 |
> |
S 32.066 |
32 |
> |
Cl 35.4527 |
33 |
> |
Ar 39.948 |
34 |
> |
Br 79.904 |
35 |
> |
Kr 83.80 |
36 |
> |
end AtomTypes |
37 |
> |
|
38 |
> |
begin DirectionalAtomTypes |
39 |
> |
//Name I_xx I_yy I_zz (All moments in (amu*Ang^2) |
40 |
> |
SSD 1.7696 0.6145 1.1550 |
41 |
> |
SSD1 1.7696 0.6145 1.1550 |
42 |
> |
SSD_E 1.7696 0.6145 1.1550 |
43 |
> |
SSD_RF 1.7696 0.6145 1.1550 |
44 |
> |
HEAD 1125 1125 250 |
45 |
> |
end DirectionalAtomTypes |
46 |
> |
|
47 |
> |
begin LennardJonesAtomTypes |
48 |
> |
//Name epsilon sigma |
49 |
> |
CH4 0.279 3.73 |
50 |
> |
CH3 0.185 3.75 |
51 |
> |
CH2 0.0866 3.95 |
52 |
> |
CH 0.0189 4.68 |
53 |
> |
SSD 0.152 3.035 |
54 |
> |
HEAD 0.185 .75 |
55 |
> |
TB1 0.0866 4.0 |
56 |
> |
TE1 0.185 4.0 |
57 |
> |
TB2 0.25 6.0 |
58 |
> |
TE2 0.5 6.0 |
59 |
> |
TB3 0.5 8.0 |
60 |
> |
TE3 0.75 8.0 |
61 |
> |
H 0.017090056482 2.81 |
62 |
> |
He 0.020269601874 2.28 |
63 |
> |
C 0.101745452544 3.35 |
64 |
> |
N 0.074123151951 3.31 |
65 |
> |
O 0.122412497592 2.95 |
66 |
> |
F 0.104924997936 2.83 |
67 |
> |
Ne 0.09339914589 2.72 |
68 |
> |
S 0.36366050421 3.52 |
69 |
> |
Cl 0.344781953445 3.35 |
70 |
> |
Ar 0.238068461226 3.41 |
71 |
> |
Br 0.511111921764 3.54 |
72 |
> |
Kr 0.32590340268 3.83 |
73 |
> |
end LennardJonesAtomTypes |
74 |
> |
|
75 |
> |
begin ElectrostaticAtomTypes |
76 |
> |
end ElectrostaticAtomTypes |
77 |
> |
|
78 |
> |
begin StickyAtomTypes |
79 |
> |
end StickyAtomTypes |
80 |
> |
|
81 |
> |
|
82 |
> |
begin BondTypes |
83 |
> |
|
84 |
> |
//Atom1 Atom2 Fixed |
85 |
> |
//V_Fixed = 0 |
86 |
> |
|
87 |
> |
//Atom1 Atom2 Harmonic b0 Kb (kcal/mol) |
88 |
> |
//V_Harmonic = Kb(b- bo)^2 |
89 |
> |
//Harmonic Examples |
90 |
> |
HEAD CH3 Harmonic 2.75 260 |
91 |
> |
HEAD CH2 Harmonic 2.75 260 |
92 |
> |
HEAD CH Harmonic 2.75 260 |
93 |
> |
HEAD TB1 Harmonic 2.76 260 |
94 |
> |
HEAD TB2 Harmonic 3.20 260 |
95 |
> |
HEAD TB3 Harmonic 3.63 260 |
96 |
> |
CH3 CH3 Harmonic 1.526 260 |
97 |
> |
CH3 CH2 Harmonic 1.526 260 |
98 |
> |
CH3 CH Harmonic 1.526 260 |
99 |
> |
CH2 CH2 Harmonic 1.526 260 |
100 |
> |
CH2 CH Harmonic 1.526 260 |
101 |
> |
CH CH Harmonic 1.526 260 |
102 |
> |
TB1 TB1 Harmonic 1.526 260 |
103 |
> |
TB2 TB2 Harmonic 2.34 260 |
104 |
> |
TB3 TB3 Harmonic 3.12 260 |
105 |
> |
TB1 TE1 Harmonic 1.526 260 |
106 |
> |
TB2 TE2 Harmonic 2.34 260 |
107 |
> |
TB3 TE3 Harmonic 3.12 260 |
108 |
> |
|
109 |
> |
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
110 |
> |
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
111 |
> |
|
112 |
> |
|
113 |
> |
//Atom1 Atom2 Quartic b0 K4 K3 K2 K1 K0 |
114 |
> |
//V_Quartic = K4(b - b0)^4 + K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
115 |
> |
|
116 |
> |
|
117 |
> |
//Atom1 Atom2 Polynomial b0 i Ki [j Kj] |
118 |
> |
//V_Quartic = Ki(b - b0)^i + Kj(b - b0)^j + ... |
119 |
> |
|
120 |
> |
|
121 |
> |
end BondTypes |
122 |
> |
|
123 |
> |
begin BendTypes |
124 |
> |
|
125 |
> |
//Harmonic |
126 |
> |
//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta |
127 |
> |
//V_Harmonic = Ktheta(Theta - Theta0)^2 |
128 |
> |
//Ktheta: kcal/mole/rad**2 |
129 |
> |
//Theta0: degrees |
130 |
> |
//Harmonic examples |
131 |
> |
HEAD CH2 HEAD Harmonic 114.0 58.84 |
132 |
> |
HEAD CH2 CH3 Harmonic 114.0 58.84 |
133 |
> |
HEAD CH2 CH2 Harmonic 114.0 58.84 |
134 |
> |
HEAD TB1 TB1 Harmonic 114.0 58.84 |
135 |
> |
HEAD TB2 TB2 Harmonic 114.0 58.84 |
136 |
> |
HEAD TB3 TB3 Harmonic 114.0 58.84 |
137 |
> |
HEAD CH2 CH Harmonic 114.0 58.84 |
138 |
> |
HEAD CH CH3 Harmonic 112.0 58.84 |
139 |
> |
HEAD CH CH2 Harmonic 112.0 58.84 |
140 |
> |
HEAD CH CH Harmonic 112.0 58.84 |
141 |
> |
CH3 CH2 CH3 Harmonic 114.0 58.84 |
142 |
> |
CH3 CH2 CH2 Harmonic 114.0 58.84 |
143 |
> |
CH3 CH2 CH Harmonic 114.0 58.84 |
144 |
> |
CH3 CH CH3 Harmonic 112.0 58.84 |
145 |
> |
CH3 CH CH2 Harmonic 112.0 58.84 |
146 |
> |
CH3 CH CH Harmonic 112.0 58.84 |
147 |
> |
CH2 CH2 CH2 Harmonic 114.0 58.84 |
148 |
> |
CH2 CH2 CH Harmonic 114.0 58.84 |
149 |
> |
CH2 CH CH2 Harmonic 112.0 58.84 |
150 |
> |
CH2 CH CH Harmonic 112.0 58.84 |
151 |
> |
CH CH2 CH Harmonic 114.0 58.84 |
152 |
> |
CH CH CH Harmonic 112.0 58.84 |
153 |
> |
TB1 TB1 TB1 Harmonic 114.0 58.84 |
154 |
> |
TB2 TB2 TB2 Harmonic 114.0 58.84 |
155 |
> |
TB3 TB3 TB3 Harmonic 114.0 58.84 |
156 |
> |
TE1 TB1 TB1 Harmonic 114.0 58.84 |
157 |
> |
TE2 TB2 TB2 Harmonic 114.0 58.84 |
158 |
> |
TE3 TB3 TB3 Harmonic 114.0 58.84 |
159 |
> |
|
160 |
> |
//GhostBend |
161 |
> |
//Atom1 Atom2 GHOST GhostBend Theta0 Ktheta |
162 |
> |
//Atom2 must be directional atom |
163 |
> |
//Ghost examples |
164 |
> |
CH2 HEAD GHOST GhostBend 129.783 0.001769723 |
165 |
> |
CH2 HEAD GHOST GhostBend 90.0 58.84 |
166 |
> |
TB1 HEAD GHOST GhostBend 90.0 58.84 |
167 |
> |
TB2 HEAD GHOST GhostBend 90.0 58.84 |
168 |
> |
TB3 HEAD GHOST GhostBend 90.0 58.84 |
169 |
> |
|
170 |
> |
//UreyBradley |
171 |
> |
//Atom1 Atom2 Atom3 UreyBradley Theta0 Ktheta S0 Kub |
172 |
> |
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
173 |
> |
//Ktheta: kcal/mole/rad**2 |
174 |
> |
//Theta0: degrees |
175 |
> |
//Kub: kcal/mole/A**2 |
176 |
> |
//S0: A |
177 |
> |
|
178 |
> |
//Cubic |
179 |
> |
//Atom1 Atom2 Atom3 Cubic Theta0 K3 K2 K1 K0 |
180 |
> |
//V_Cubic = K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
181 |
> |
|
182 |
> |
//Quartic |
183 |
> |
//Atom1 Atom2 Atom3 Quartic Theta0 K4 K3 K2 K1 K0 |
184 |
> |
//V_Quartic = K4(Theta - Theta0)^4 + K3(Theta - Theta0)^3 + K2(Theta - Theta0)^2 + K1(Theta - Theta0) + K0 |
185 |
> |
|
186 |
> |
//Polynomial |
187 |
> |
//Atom1 Atom2 Atom3 Polynomial Theta0 i Ki [j Kj] |
188 |
> |
//V_Polynomial = Ki(Theta - Theta0)^i + Kj(Theta - Theta0)^j + ... |
189 |
> |
|
190 |
> |
end BendTypes |
191 |
> |
|
192 |
> |
begin TorsionTypes |
193 |
> |
|
194 |
> |
//Cubic |
195 |
> |
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
196 |
> |
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
197 |
> |
//Cubic Examples |
198 |
> |
HEAD CH2 CH2 HEAD Cubic 5.9602 -0.2568 -3.802 2.1586 |
199 |
> |
HEAD CH2 CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
200 |
> |
HEAD CH CH HEAD Cubic 3.3254 -0.4215 -1.686 1.1661 |
201 |
> |
HEAD CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
202 |
> |
HEAD CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
203 |
> |
HEAD CH CH2 CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
204 |
> |
HEAD CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
205 |
> |
HEAD CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
206 |
> |
HEAD CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
207 |
> |
HEAD CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
208 |
> |
HEAD CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
209 |
> |
HEAD CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
210 |
> |
HEAD CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
211 |
> |
HEAD CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
212 |
> |
HEAD CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
213 |
> |
HEAD TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
214 |
> |
HEAD TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
215 |
> |
HEAD TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
216 |
> |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
217 |
> |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
218 |
> |
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
219 |
> |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
220 |
> |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
221 |
> |
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
222 |
> |
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
223 |
> |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
224 |
> |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
225 |
> |
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
226 |
> |
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
227 |
> |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
228 |
> |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
229 |
> |
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
230 |
> |
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
231 |
> |
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
232 |
> |
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
233 |
> |
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
234 |
> |
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
235 |
> |
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
236 |
> |
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
237 |
> |
TB1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
238 |
> |
TB2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
239 |
> |
TB3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
240 |
> |
TE1 TB1 TB1 TB1 Cubic 5.9602 -0.2568 -3.802 2.1586 |
241 |
> |
TE2 TB2 TB2 TB2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
242 |
> |
TE3 TB3 TB3 TB3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
243 |
> |
|
244 |
> |
//Charmm |
245 |
> |
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
246 |
> |
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
247 |
> |
//Kchi: kcal/mole |
248 |
> |
//n: multiplicity |
249 |
> |
//delta: degrees |
250 |
> |
//in some cases, a Charmm may have two or three terms. If n is equal to 0, it falls back to harmonic form |
251 |
> |
|
252 |
> |
//Quartic |
253 |
> |
//Atom1 Atom2 Atom3 Atom4 Quartic k4 k3 k2 k1 k0 ( all are kcal/mol ) |
254 |
> |
//V_Quartic = k4(cos phi)^4 + k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
255 |
> |
|
256 |
> |
//Polynomial |
257 |
> |
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
258 |
> |
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
259 |
> |
|
260 |
> |
end TorsionTypes |
261 |
> |
|
262 |
> |
|