--- trunk/tcProps/rmsd.c	2004/03/02 22:15:53	1079
+++ trunk/tcProps/rmsd.c	2004/03/03 15:16:15	1080
@@ -56,6 +56,8 @@ void rmsd( enum atomNames rType, double startTime, cha
   double rmsdDt;
   double timeOut, outVal;
 
+  struct atomCoord* atoms;
+
   framesFinished = 0;
   
   startFound = 0;
@@ -91,9 +93,84 @@ void rmsd( enum atomNames rType, double startTime, cha
 	       index,
 	       corrFrames );
     }
-   
+     
+    // initialize the arrays
+    
+    atoms = myFrames[index].atoms;
+    for(j=0;j<nLipids;j++){
+      
+      atoms[nLipAtoms*j+0].type = HEAD;
+      atoms[nLipAtoms*j+0].mass = 72;
+      atoms[nLipAtoms*j+0].u[0] = 0.0;
+      atoms[nLipAtoms*j+0].u[1] = 0.0;
+      atoms[nLipAtoms*j+0].u[2] = 1.0;
+      
+      
+      
+      atoms[nLipAtoms*j+1].type = CH2;
+      atoms[nLipAtoms*j+1].mass = 14.03;
+      
+      atoms[nLipAtoms*j+2].type = CH;
+      atoms[nLipAtoms*j+2].mass = 13.02;
+      
+      atoms[nLipAtoms*j+3].type = CH2;
+      atoms[nLipAtoms*j+3].mass = 14.03;
+      
+      atoms[nLipAtoms*j+4].type = CH2;
+      atoms[nLipAtoms*j+4].mass = 14.03;
+      
+      atoms[nLipAtoms*j+5].type = CH2;
+      atoms[nLipAtoms*j+5].mass = 14.03;
+      
+      atoms[nLipAtoms*j+6].type = CH2;
+      atoms[nLipAtoms*j+6].mass = 14.03;
+      
+      atoms[nLipAtoms*j+7].type = CH2;
+      atoms[nLipAtoms*j+7].mass = 14.03;
+      
+      atoms[nLipAtoms*j+8].type = CH2;
+      atoms[nLipAtoms*j+8].mass = 14.03;
+      
+      atoms[nLipAtoms*j+9].type = CH2;
+      atoms[nLipAtoms*j+9].mass = 14.03;
+      
+      atoms[nLipAtoms*j+10].type = CH3;
+      atoms[nLipAtoms*j+10].mass = 15.04;
+      
+      atoms[nLipAtoms*j+11].type = CH2;
+      atoms[nLipAtoms*j+11].mass = 14.03;
+      
+      atoms[nLipAtoms*j+12].type = CH2;
+      atoms[nLipAtoms*j+12].mass = 14.03;
+      
+      atoms[nLipAtoms*j+13].type = CH2;    
+      atoms[nLipAtoms*j+13].mass = 14.03;
+      
+      atoms[nLipAtoms*j+14].type = CH2;
+      atoms[nLipAtoms*j+14].mass = 14.03;
+      
+      atoms[nLipAtoms*j+15].type = CH2;
+      atoms[nLipAtoms*j+15].mass = 14.03;
+      
+      atoms[nLipAtoms*j+16].type = CH2;
+      atoms[nLipAtoms*j+16].mass = 14.03;
+      
+      atoms[nLipAtoms*j+17].type = CH2;
+      atoms[nLipAtoms*j+17].mass = 14.03;
+      
+      atoms[nLipAtoms*j+18].type = CH3;
+      atoms[nLipAtoms*j+18].mass = 15.04;
+    }
+    
+    for(j=(nLipAtoms*nLipids);j<nAtoms;j++){
+      atoms[j].type = SSD;
+      atoms[j].mass = 18.03;
+      atoms[j].u[0] = 0.0;
+      atoms[j].u[1] = 0.0;
+      atoms[j].u[2] = 1.0;
+    }
     myFrames[index].time = frameTimes[i];
-    readFrame(i, myFrames[index].atoms, myFrames[index].Hmat );
+    readFrame(i, atoms, myFrames[index].Hmat );
   }
 
   // initialize the counts and the correlation