samples/dipole/Lipid.frc

begin AtomTypes    
//Name          mass     (amu)
CH4             16.05           
CH3             15.04           
CH2             14.03           
CH              13.02
CE              28.01           //C-O
CK              28.01           //C=O
HDP             14.03           //Head Dipole 
NC4             73.137  //CH2-N(CH3)3
PO4             108.995         //PO4-CH2
SSD             18.0153         
SSD1            18.0153 
SSD_E           18.0153
SSD_RF          18.0153
end AtomTypes


begin DirectionalAtomTypes
//Name          I_xx    I_yy    I_zz    (All moments in (amu*Ang^2)
SSD             1.7696  0.6145  1.1550  
SSD1            1.7696  0.6145  1.1550  
SSD_E           1.7696  0.6145  1.1550  
SSD_RF          1.7696  0.6145  1.1550  
HDP             2.221   0.0     2.221           
CE              13.643  13.643  0.0
CK              10.161  10.161  0.0
end DirectionalAtomTypes  

begin LennardJonesAtomTypes
//Name  epsilon sigma   
SSD     0.152   3.051                                   
SSD1    0.152   3.016 
SSD_E   0.152   3.035
SSD_RF  0.152   3.019 

//CH3   3.75    98.0
//CH2   3.94    46.0
//CH    4.33    10.0
CH3     0.195   3.75
CH2     0.0914  3.95
CH      0.0199  4.68    
CK      0.311   3.592
CE      0.294   3.427
PO4     0.543   4.55    
NC4     1.1     4.11   
HDP     0.0914  3.95            
end LennardJonesAtomTypes

begin ChargeAtomTypes
// name charge
end ChargeAtomTypes

begin MultipoleAtomTypes
//only support up tp quadrupole.
//possible format: 
// name d theta phi psi dipole_moment
// name s theta phi psi dipole_moment splitdipole_distance
// name q theta phi psi Qxx Qyy Qzz
// name dq theta phi psi dipole_moment Qxx Qyy Qzz
// name sq theta phi psi dipole_moment splitdipole_distance Qxx Qyy Qzz
// euler angles are given in units of degree 
// dipoles are given in units of Debye
// split dipole distances are given in units of Angstrom
// quadrupoles are given in units of 
// 
SSD_E   d       0.0     0.0     0.0     2.42
SSD_RF  d       0.0     0.0     0.0     2.48
SSD     d       0.0     0.0     0.0     2.35
SSD1    d       0.0     0.0     0.0     2.35
CE      d       0.0     0.0     0.0     1.693
CK      d       0.0     0.0     0.0     2.478
HDP     s       0.0     0.0     0.0     20.6    4.63
end MultipoleAtomTypes


begin BondTypes

//Atom1 Atom2   Fixed
//V_Fixed = 0

//Atom1 Atom2   Harmonic        b0      Kb (kcal/mol)
//V_Harmonic = 0.5*Kb(b- bo)^2
//Harmonic Examples

//CHx-CHy       1.54
CH3     CH3     Harmonic        1.54    260
CH3     CH2     Harmonic        1.54    260
CH3     CH      Harmonic        1.54    260
CH2     CH2     Harmonic        1.54    260
CH2     CH      Harmonic        1.54    260
CH      CH      Harmonic        1.54    260

PO4     CH2     Harmonic        2.67    260
CH2     CE      Harmonic        1.54    260             
CE      CE      Harmonic        2.27    260
CE      CK      Harmonic        2.08    317

//CHx-C aldehyde/ketone 1.52
CH3     CK      Harmonic        1.52    317
CH2     CK      Harmonic        1.52    317
CH      CK      Harmonic        1.52    317

end BondTypes

begin BendTypes

//Harmonic
//Atom1 Atom2   Atom3   Harmonic        Theta0  Ktheta
//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2
//Ktheta: kcal/mole/rad**2
//Theta0: degrees
//Harmonic examples

//CHx-CH2-CHy   114     62500 (ktheta/kb)
CH3     CH2     CH3     Harmonic        114.0   124.15
CH3     CH2     CH2     Harmonic        114.0   124.15
CH3     CH2     CH      Harmonic        114.0   124.15
CH2     CH2     CH2     Harmonic        114.0   124.15
CH2     CH2     CH      Harmonic        114.0   124.15
CH      CH2     CH      Harmonic        114.0   124.15

//CHx-CH-CHy    112     62500 (ktheta/kb)
CH3     CH      CH3     Harmonic        112.0   124.15
CH3     CH      CH2     Harmonic        112.0   124.15
CH3     CH      CH      Harmonic        112.0   124.15
CH2     CH      CH3     Harmonic        112.0   124.15
CH2     CH      CH2     Harmonic        112.0   124.15
CH2     CH      CH      Harmonic        112.0   124.15
CH      CH      CH3     Harmonic        112.0   124.15
CH      CH      CH2     Harmonic        112.0   124.15
CH      CH      CH      Harmonic        112.0   124.15

//CHx-C(=O)-CHy 117.2   62500
CH3     CK      CH3     Harmonic        117.2   124.15
CH3     CK      CH2     Harmonic        117.2   124.15
CH3     CK      CH      Harmonic        117.2   124.15
CH2     CK      CH2     Harmonic        117.2   124.15
CH2     CK      CH      Harmonic        117.2   124.15
CH      CK      CH      Harmonic        117.2   124.15
CE      CK      CH3     Harmonic        117.2   124.15
CE      CK      CH2     Harmonic        117.2   124.15
CE      CK      CH      Harmonic        117.2   124.15

CH2     CH2     CK      Harmonic        114     124.15
CE      CE      CK      Harmonic        114     124.15
CH2     CE      CE      Harmonic        117.2   124.15
CH2     CE      CK      Harmonic        114     124.15

PO4     CH2     CE      Harmonic        180.0   124.15
//GhostBend
//Atom1 Atom2   GHOST   GhostBend       Theta0  Ktheta
//Atom2 must be directional atom
//Ghost examples
CH2     HDP     GHOST   GhostBend       129.783 0.00354
NC4     PO4     CH2     Harmonic        98.03   20.00 
//CHx-C=O       121.4   62500
//since the dipole direction is from Oxygen to carbon in CK
//The equilibrium angle becomes its supplementary angle 
CH3     CK      GHOST   GhostBend       58.6    124.15
CH2     CK      GHOST   GhostBend       58.6    124.15
CH      CK      GHOST   GhostBend       58.6    124.15
CH2     CE      GHOST   GhostBend       68.0    119.98  
end BendTypes

begin TorsionTypes

//Cubic
//Atom1 Atom2   Atom3   Atom4   Cubic           k3              k2              k1              k0  ( all are kcal/mol )
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0
//Cubic Examples
//CHx-CH2-CH2-CHy       0       335.05  -68.19  791.32
CH3     CH2     CH2     CH3     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH2     CH      CH3     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH      CH      CH3     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH2     CH2     CH2     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH2     CH      CH2     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH      CH2     CH2     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH      CH      CH2     Cubic           6.287   0.2709  -4.050  2.237
CH3     CH2     CH2     CH      Cubic           6.287   0.2709  -4.050  2.237
CH3     CH2     CH      CH      Cubic           6.287   0.2709  -4.050  2.237
CH3     CH      CH2     CH      Cubic           6.287   0.2709  -4.050  2.237
CH3     CH      CH      CH      Cubic           6.287   0.2709  -4.050  2.237
CH2     CH2     CH2     CH2     Cubic           6.287   0.2709  -4.050  2.237
CH2     CH2     CH      CH2     Cubic           6.287   0.2709  -4.050  2.237
CH2     CH      CH      CH2     Cubic           6.287   0.2709  -4.050  2.237
CH2     CH2     CH2     CH      Cubic           6.287   0.2709  -4.050  2.237
CH2     CH2     CH      CH      Cubic           6.287   0.2709  -4.050  2.237
CH2     CH      CH2     CH      Cubic           6.287   0.2709  -4.050  2.237
CH2     CH      CH      CH      Cubic           6.287   0.2709  -4.050  2.237
CH      CH2     CH2     CH      Cubic           6.287   0.2709  -4.050  2.237
CH      CH2     CH      CH      Cubic           6.287   0.2709  -4.050  2.237
CH      CH      CH      CH      Cubic           6.287   0.2709  -4.050  2.237
CK      CH2     CH2     CH2     Cubic           6.287   0.2709  -4.050  2.237           

//CHx-CH2-CH2-O         0       176.62  -53.34  769.93
CE      CK      CH2     CH2     Cubic           6.118   0.212   -4.237  1.668 
CH2     CE      CE      GHOST   GhostTorsion    6.118   0.212   -4.237  1.668
CH2     CE      CK      GHOST   GhostTorsion    6.118   0.212   -4.237  1.668

//CHx-CHy-C=O           2035.58 -736.90 57.84   -293.23
CH3     CH2     CK      GHOST   GhostTorsion    -2.330  -0.230  0.284   2.227
CH3     CH      CK      GHOST   GhostTorsion    -2.330  -0.230  0.284   2.227
CH2     CH2     CK      GHOST   GhostTorsion    -2.330  -0.230  0.284   2.227
CH      CH      CK      GHOST   GhostTorsion    -2.330  -0.230  0.284   2.227

end TorsionTypes


Revision:	2106
Committed:	Thu Mar 10 18:44:02 2005 UTC (20 years, 8 months ago) by tim
File size:	5732 byte(s)
Log Message:	adding test case for split dipole
#	User	Rev	Content
1	tim	2106	begin AtomTypes
2			//Name mass (amu)
3			CH4 16.05
4			CH3 15.04
5			CH2 14.03
6			CH 13.02
7			CE 28.01 //C-O
8			CK 28.01 //C=O
9			HDP 14.03 //Head Dipole
10			NC4 73.137 //CH2-N(CH3)3
11			PO4 108.995 //PO4-CH2
12			SSD 18.0153
13			SSD1 18.0153
14			SSD_E 18.0153
15			SSD_RF 18.0153
16			end AtomTypes
17
18
19
20			begin DirectionalAtomTypes
21			//Name I_xx I_yy I_zz (All moments in (amu*Ang^2)
22			SSD 1.7696 0.6145 1.1550
23			SSD1 1.7696 0.6145 1.1550
24			SSD_E 1.7696 0.6145 1.1550
25			SSD_RF 1.7696 0.6145 1.1550
26			HDP 2.221 0.0 2.221
27			CE 13.643 13.643 0.0
28			CK 10.161 10.161 0.0
29			end DirectionalAtomTypes
30
31			begin LennardJonesAtomTypes
32			//Name epsilon sigma
33			SSD 0.152 3.051
34			SSD1 0.152 3.016
35			SSD_E 0.152 3.035
36			SSD_RF 0.152 3.019
37
38			//CH3 3.75 98.0
39			//CH2 3.94 46.0
40			//CH 4.33 10.0
41			CH3 0.195 3.75
42			CH2 0.0914 3.95
43			CH 0.0199 4.68
44			CK 0.311 3.592
45			CE 0.294 3.427
46			PO4 0.543 4.55
47			NC4 1.1 4.11
48			HDP 0.0914 3.95
49			end LennardJonesAtomTypes
50
51			begin ChargeAtomTypes
52			// name charge
53			end ChargeAtomTypes
54
55			begin MultipoleAtomTypes
56			//only support up tp quadrupole.
57			//possible format:
58			// name d theta phi psi dipole_moment
59			// name s theta phi psi dipole_moment splitdipole_distance
60			// name q theta phi psi Qxx Qyy Qzz
61			// name dq theta phi psi dipole_moment Qxx Qyy Qzz
62			// name sq theta phi psi dipole_moment splitdipole_distance Qxx Qyy Qzz
63			// euler angles are given in units of degree
64			// dipoles are given in units of Debye
65			// split dipole distances are given in units of Angstrom
66			// quadrupoles are given in units of
67			//
68			SSD_E d 0.0 0.0 0.0 2.42
69			SSD_RF d 0.0 0.0 0.0 2.48
70			SSD d 0.0 0.0 0.0 2.35
71			SSD1 d 0.0 0.0 0.0 2.35
72			CE d 0.0 0.0 0.0 1.693
73			CK d 0.0 0.0 0.0 2.478
74			HDP s 0.0 0.0 0.0 20.6 4.63
75			end MultipoleAtomTypes
76
77
78			begin BondTypes
79
80			//Atom1 Atom2 Fixed
81			//V_Fixed = 0
82
83			//Atom1 Atom2 Harmonic b0 Kb (kcal/mol)
84			//V_Harmonic = 0.5*Kb(b- bo)^2
85			//Harmonic Examples
86
87			//CHx-CHy 1.54
88			CH3 CH3 Harmonic 1.54 260
89			CH3 CH2 Harmonic 1.54 260
90			CH3 CH Harmonic 1.54 260
91			CH2 CH2 Harmonic 1.54 260
92			CH2 CH Harmonic 1.54 260
93			CH CH Harmonic 1.54 260
94
95			PO4 CH2 Harmonic 2.67 260
96			CH2 CE Harmonic 1.54 260
97			CE CE Harmonic 2.27 260
98			CE CK Harmonic 2.08 317
99
100			//CHx-C aldehyde/ketone 1.52
101			CH3 CK Harmonic 1.52 317
102			CH2 CK Harmonic 1.52 317
103			CH CK Harmonic 1.52 317
104
105			end BondTypes
106
107			begin BendTypes
108
109			//Harmonic
110			//Atom1 Atom2 Atom3 Harmonic Theta0 Ktheta
111			//V_Harmonic = 0.5*Ktheta(Theta - Theta0)^2
112			//Ktheta: kcal/mole/rad**2
113			//Theta0: degrees
114			//Harmonic examples
115
116			//CHx-CH2-CHy 114 62500 (ktheta/kb)
117			CH3 CH2 CH3 Harmonic 114.0 124.15
118			CH3 CH2 CH2 Harmonic 114.0 124.15
119			CH3 CH2 CH Harmonic 114.0 124.15
120			CH2 CH2 CH2 Harmonic 114.0 124.15
121			CH2 CH2 CH Harmonic 114.0 124.15
122			CH CH2 CH Harmonic 114.0 124.15
123
124			//CHx-CH-CHy 112 62500 (ktheta/kb)
125			CH3 CH CH3 Harmonic 112.0 124.15
126			CH3 CH CH2 Harmonic 112.0 124.15
127			CH3 CH CH Harmonic 112.0 124.15
128			CH2 CH CH3 Harmonic 112.0 124.15
129			CH2 CH CH2 Harmonic 112.0 124.15
130			CH2 CH CH Harmonic 112.0 124.15
131			CH CH CH3 Harmonic 112.0 124.15
132			CH CH CH2 Harmonic 112.0 124.15
133			CH CH CH Harmonic 112.0 124.15
134
135			//CHx-C(=O)-CHy 117.2 62500
136			CH3 CK CH3 Harmonic 117.2 124.15
137			CH3 CK CH2 Harmonic 117.2 124.15
138			CH3 CK CH Harmonic 117.2 124.15
139			CH2 CK CH2 Harmonic 117.2 124.15
140			CH2 CK CH Harmonic 117.2 124.15
141			CH CK CH Harmonic 117.2 124.15
142			CE CK CH3 Harmonic 117.2 124.15
143			CE CK CH2 Harmonic 117.2 124.15
144			CE CK CH Harmonic 117.2 124.15
145
146			CH2 CH2 CK Harmonic 114 124.15
147			CE CE CK Harmonic 114 124.15
148			CH2 CE CE Harmonic 117.2 124.15
149			CH2 CE CK Harmonic 114 124.15
150
151			PO4 CH2 CE Harmonic 180.0 124.15
152			//GhostBend
153			//Atom1 Atom2 GHOST GhostBend Theta0 Ktheta
154			//Atom2 must be directional atom
155			//Ghost examples
156			CH2 HDP GHOST GhostBend 129.783 0.00354
157			NC4 PO4 CH2 Harmonic 98.03 20.00
158			//CHx-C=O 121.4 62500
159			//since the dipole direction is from Oxygen to carbon in CK
160			//The equilibrium angle becomes its supplementary angle
161			CH3 CK GHOST GhostBend 58.6 124.15
162			CH2 CK GHOST GhostBend 58.6 124.15
163			CH CK GHOST GhostBend 58.6 124.15
164			CH2 CE GHOST GhostBend 68.0 119.98
165			end BendTypes
166
167			begin TorsionTypes
168
169			//Cubic
170			//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol )
171			//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0
172			//Cubic Examples
173			//CHx-CH2-CH2-CHy 0 335.05 -68.19 791.32
174			CH3 CH2 CH2 CH3 Cubic 6.287 0.2709 -4.050 2.237
175			CH3 CH2 CH CH3 Cubic 6.287 0.2709 -4.050 2.237
176			CH3 CH CH CH3 Cubic 6.287 0.2709 -4.050 2.237
177			CH3 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237
178			CH3 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237
179			CH3 CH CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237
180			CH3 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237
181			CH3 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237
182			CH3 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237
183			CH3 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237
184			CH3 CH CH CH Cubic 6.287 0.2709 -4.050 2.237
185			CH2 CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237
186			CH2 CH2 CH CH2 Cubic 6.287 0.2709 -4.050 2.237
187			CH2 CH CH CH2 Cubic 6.287 0.2709 -4.050 2.237
188			CH2 CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237
189			CH2 CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237
190			CH2 CH CH2 CH Cubic 6.287 0.2709 -4.050 2.237
191			CH2 CH CH CH Cubic 6.287 0.2709 -4.050 2.237
192			CH CH2 CH2 CH Cubic 6.287 0.2709 -4.050 2.237
193			CH CH2 CH CH Cubic 6.287 0.2709 -4.050 2.237
194			CH CH CH CH Cubic 6.287 0.2709 -4.050 2.237
195			CK CH2 CH2 CH2 Cubic 6.287 0.2709 -4.050 2.237
196
197			//CHx-CH2-CH2-O 0 176.62 -53.34 769.93
198			CE CK CH2 CH2 Cubic 6.118 0.212 -4.237 1.668
199			CH2 CE CE GHOST GhostTorsion 6.118 0.212 -4.237 1.668
200			CH2 CE CK GHOST GhostTorsion 6.118 0.212 -4.237 1.668
201
202			//CHx-CHy-C=O 2035.58 -736.90 57.84 -293.23
203			CH3 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227
204			CH3 CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227
205			CH2 CH2 CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227
206			CH CH CK GHOST GhostTorsion -2.330 -0.230 0.284 2.227
207
208			end TorsionTypes
209
210