56 |
|
double rmsdDt; |
57 |
|
double timeOut, outVal; |
58 |
|
|
59 |
+ |
struct atomCoord* atoms; |
60 |
+ |
|
61 |
|
framesFinished = 0; |
62 |
|
|
63 |
|
startFound = 0; |
93 |
|
index, |
94 |
|
corrFrames ); |
95 |
|
} |
96 |
< |
|
96 |
> |
|
97 |
> |
// initialize the arrays |
98 |
> |
|
99 |
> |
atoms = myFrames[index].atoms; |
100 |
> |
for(j=0;j<nLipids;j++){ |
101 |
> |
|
102 |
> |
atoms[nLipAtoms*j+0].type = HEAD; |
103 |
> |
atoms[nLipAtoms*j+0].mass = 72; |
104 |
> |
atoms[nLipAtoms*j+0].u[0] = 0.0; |
105 |
> |
atoms[nLipAtoms*j+0].u[1] = 0.0; |
106 |
> |
atoms[nLipAtoms*j+0].u[2] = 1.0; |
107 |
> |
|
108 |
> |
|
109 |
> |
|
110 |
> |
atoms[nLipAtoms*j+1].type = CH2; |
111 |
> |
atoms[nLipAtoms*j+1].mass = 14.03; |
112 |
> |
|
113 |
> |
atoms[nLipAtoms*j+2].type = CH; |
114 |
> |
atoms[nLipAtoms*j+2].mass = 13.02; |
115 |
> |
|
116 |
> |
atoms[nLipAtoms*j+3].type = CH2; |
117 |
> |
atoms[nLipAtoms*j+3].mass = 14.03; |
118 |
> |
|
119 |
> |
atoms[nLipAtoms*j+4].type = CH2; |
120 |
> |
atoms[nLipAtoms*j+4].mass = 14.03; |
121 |
> |
|
122 |
> |
atoms[nLipAtoms*j+5].type = CH2; |
123 |
> |
atoms[nLipAtoms*j+5].mass = 14.03; |
124 |
> |
|
125 |
> |
atoms[nLipAtoms*j+6].type = CH2; |
126 |
> |
atoms[nLipAtoms*j+6].mass = 14.03; |
127 |
> |
|
128 |
> |
atoms[nLipAtoms*j+7].type = CH2; |
129 |
> |
atoms[nLipAtoms*j+7].mass = 14.03; |
130 |
> |
|
131 |
> |
atoms[nLipAtoms*j+8].type = CH2; |
132 |
> |
atoms[nLipAtoms*j+8].mass = 14.03; |
133 |
> |
|
134 |
> |
atoms[nLipAtoms*j+9].type = CH2; |
135 |
> |
atoms[nLipAtoms*j+9].mass = 14.03; |
136 |
> |
|
137 |
> |
atoms[nLipAtoms*j+10].type = CH3; |
138 |
> |
atoms[nLipAtoms*j+10].mass = 15.04; |
139 |
> |
|
140 |
> |
atoms[nLipAtoms*j+11].type = CH2; |
141 |
> |
atoms[nLipAtoms*j+11].mass = 14.03; |
142 |
> |
|
143 |
> |
atoms[nLipAtoms*j+12].type = CH2; |
144 |
> |
atoms[nLipAtoms*j+12].mass = 14.03; |
145 |
> |
|
146 |
> |
atoms[nLipAtoms*j+13].type = CH2; |
147 |
> |
atoms[nLipAtoms*j+13].mass = 14.03; |
148 |
> |
|
149 |
> |
atoms[nLipAtoms*j+14].type = CH2; |
150 |
> |
atoms[nLipAtoms*j+14].mass = 14.03; |
151 |
> |
|
152 |
> |
atoms[nLipAtoms*j+15].type = CH2; |
153 |
> |
atoms[nLipAtoms*j+15].mass = 14.03; |
154 |
> |
|
155 |
> |
atoms[nLipAtoms*j+16].type = CH2; |
156 |
> |
atoms[nLipAtoms*j+16].mass = 14.03; |
157 |
> |
|
158 |
> |
atoms[nLipAtoms*j+17].type = CH2; |
159 |
> |
atoms[nLipAtoms*j+17].mass = 14.03; |
160 |
> |
|
161 |
> |
atoms[nLipAtoms*j+18].type = CH3; |
162 |
> |
atoms[nLipAtoms*j+18].mass = 15.04; |
163 |
> |
} |
164 |
> |
|
165 |
> |
for(j=(nLipAtoms*nLipids);j<nAtoms;j++){ |
166 |
> |
atoms[j].type = SSD; |
167 |
> |
atoms[j].mass = 18.03; |
168 |
> |
atoms[j].u[0] = 0.0; |
169 |
> |
atoms[j].u[1] = 0.0; |
170 |
> |
atoms[j].u[2] = 1.0; |
171 |
> |
} |
172 |
|
myFrames[index].time = frameTimes[i]; |
173 |
< |
readFrame(i, myFrames[index].atoms, myFrames[index].Hmat ); |
173 |
> |
readFrame(i, atoms, myFrames[index].Hmat ); |
174 |
|
} |
175 |
|
|
176 |
|
// initialize the counts and the correlation |