water/dimer/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

molecule{
  name = "Cl-";
  nAtoms = 1;
  atom[0]{
    type = "Cl-";
    position(0.0, 0.0, 0.0);
  }
}

molecule{
  name = "Na+";
  nAtoms = 1;
  atom[0]{
    type = "Na+";
    position(0.0, 0.0, 0.0);
  }
}

molecule{
  name = "SSD_E";
  nAtoms = 1;
  atom[0]{
    type = "SSD_E";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD_RF";
  nAtoms = 1;
  atom[0]{
    type = "SSD_RF";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD";
  nAtoms = 1;
  atom[0]{
    type = "SSD";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD1";
  nAtoms = 1;
  atom[0]{
    type = "SSD1";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TAP";
  nAtoms = 1;
  atom[0]{
    type = "TAP";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TIP3P";
  nAtoms = 3;
  atom[0]{
    type = "O_TIP3P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP3P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP3P";
    position( 0.0, -0.75695, 0.52032 );
  }

  nRigidBodies = 1;
  rigidBody[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "TIP4P";
  nAtoms = 4;
  atom[0]{
    type = "O_TIP4P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP4P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP4P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP4P";
    position( 0.0, 0.0, 0.08444 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{ 
    nMembers = 4;
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP5P";
  nAtoms = 5;
  atom[0]{
    type = "O_TIP5P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP5P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP5P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP5P";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = "EP_TIP5P";
    position( -0.57154, 0.0, -0.46971 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{ 
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "SPCE";
  nAtoms = 3;
  atom[0]{
    type = "O_SPCE";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPCE";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPCE";
    position( 0.0, -0.81649, 0.51275 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

}

molecule{
  name = "DPD";
  nAtoms = 1;
  atom[0]{
    type = "DPD";
    position(0.0, 0.0, 0.0);
  }
}

#endif
Revision:	2229
Committed:	Tue May 17 22:35:01 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	3069 byte(s)
Log Message:	Modifications to tap. Also correcting changes to the previous merge that were not caught
#	User	Rev	Content
1	gezelter	1490	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4			molecule{
5	chrisfen	2152	name = "Cl-";
6	gezelter	2084	nAtoms = 1;
7			atom[0]{
8	chrisfen	2152	type = "Cl-";
9	gezelter	2084	position(0.0, 0.0, 0.0);
10			}
11			}
12
13			molecule{
14	chrisfen	2152	name = "Na+";
15			nAtoms = 1;
16			atom[0]{
17			type = "Na+";
18			position(0.0, 0.0, 0.0);
19			}
20			}
21
22			molecule{
23	gezelter	1490	name = "SSD_E";
24			nAtoms = 1;
25			atom[0]{
26			type = "SSD_E";
27			position( 0.0, 0.0, 0.0 );
28			orientation( 0.0, 0.0, 0.0 );
29			}
30			}
31
32			molecule{
33			name = "SSD_RF";
34			nAtoms = 1;
35			atom[0]{
36			type = "SSD_RF";
37			position( 0.0, 0.0, 0.0 );
38			orientation( 0.0, 0.0, 0.0 );
39			}
40			}
41
42			molecule{
43			name = "SSD";
44			nAtoms = 1;
45			atom[0]{
46			type = "SSD";
47			position( 0.0, 0.0, 0.0 );
48			orientation( 0.0, 0.0, 0.0 );
49			}
50			}
51
52			molecule{
53			name = "SSD1";
54			nAtoms = 1;
55			atom[0]{
56			type = "SSD1";
57			position( 0.0, 0.0, 0.0 );
58			orientation( 0.0, 0.0, 0.0 );
59			}
60			}
61
62			molecule{
63	chrisfen	2229	name = "TAP";
64			nAtoms = 1;
65			atom[0]{
66			type = "TAP";
67			position( 0.0, 0.0, 0.0 );
68			orientation( 0.0, 0.0, 0.0 );
69			}
70			}
71
72			molecule{
73	gezelter	1490	name = "TIP3P";
74			nAtoms = 3;
75			atom[0]{
76			type = "O_TIP3P";
77			position( 0.0, 0.0, -0.06556 );
78			}
79			atom[1]{
80			type = "H_TIP3P";
81			position( 0.0, 0.75695, 0.52032 );
82			}
83			atom[2]{
84			type = "H_TIP3P";
85			position( 0.0, -0.75695, 0.52032 );
86			}
87
88			nRigidBodies = 1;
89			rigidBody[0]{
90			nMembers = 3;
91			members(0, 1, 2);
92			}
93
94			nCutoffGroups = 1;
95	chrisfen	2152	cutoffGroup[0]{
96	gezelter	1490	nMembers = 3;
97			members(0, 1, 2);
98			}
99			}
100
101			molecule{
102			name = "TIP4P";
103			nAtoms = 4;
104			atom[0]{
105			type = "O_TIP4P";
106			position( 0.0, 0.0, -0.06556 );
107			}
108			atom[1]{
109			type = "H_TIP4P";
110			position( 0.0, 0.75695, 0.52032 );
111			}
112			atom[2]{
113			type = "H_TIP4P";
114			position( 0.0, -0.75695, 0.52032 );
115			}
116			atom[3]{
117			type = "EP_TIP4P";
118			position( 0.0, 0.0, 0.08444 );
119			}
120			nRigidBodies = 1;
121			rigidBody[0]{
122			nMembers = 4;
123			members(0, 1, 2, 3);
124			}
125
126			nCutoffGroups = 1;
127	chrisfen	2152	cutoffGroup[0]{
128	gezelter	1490	nMembers = 4;
129			members(0, 1, 2, 3);
130			}
131			}
132
133			molecule{
134			name = "TIP5P";
135			nAtoms = 5;
136			atom[0]{
137			type = "O_TIP5P";
138			position( 0.0, 0.0, -0.06556 );
139			}
140			atom[1]{
141			type = "H_TIP5P";
142			position( 0.0, 0.75695, 0.52032 );
143			}
144			atom[2]{
145			type = "H_TIP5P";
146			position( 0.0, -0.75695, 0.52032 );
147			}
148			atom[3]{
149			type = "EP_TIP5P";
150			position( 0.57154, 0.0, -0.46971 );
151			}
152			atom[4]{
153			type = "EP_TIP5P";
154			position( -0.57154, 0.0, -0.46971 );
155			}
156			nRigidBodies = 1;
157			rigidBody[0]{
158			nMembers = 5;
159			members(0, 1, 2, 3, 4);
160			}
161
162			nCutoffGroups = 1;
163	chrisfen	2152	cutoffGroup[0]{
164	gezelter	1490	nMembers = 5;
165			members(0, 1, 2, 3, 4);
166			}
167			}
168
169			molecule{
170			name = "SPCE";
171			nAtoms = 3;
172			atom[0]{
173			type = "O_SPCE";
174			position( 0.0, 0.0, -0.06461 );
175			}
176			atom[1]{
177			type = "H_SPCE";
178			position( 0.0, 0.81649, 0.51275 );
179			}
180			atom[2]{
181			type = "H_SPCE";
182			position( 0.0, -0.81649, 0.51275 );
183			}
184			nRigidBodies = 1;
185			rigidBody[0]{
186			nMembers = 3;
187			members(0, 1, 2);
188			}
189
190			nCutoffGroups = 1;
191	chrisfen	2152	cutoffGroup[0]{
192	gezelter	1490	nMembers = 3;
193			members(0, 1, 2);
194			}
195
196			}
197
198			molecule{
199			name = "DPD";
200			nAtoms = 1;
201			atom[0]{
202			type = "DPD";
203			position(0.0, 0.0, 0.0);
204			}
205			}
206
207			#endif