diff --git a/compdist.C b/compdist.C
deleted file mode 100644
index 6420e2d..0000000
--- a/compdist.C
+++ /dev/null
@@ -1,167 +0,0 @@
-/* Program written by Giovanni Pinamonti
-  PhD student at 
-  Scuola Internazionale Superiori di Studi Avanzati, Trieste, Italy
-   begin june 11th 2013 */
-
-#include <fstream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#include <malloc.h>
-#include <string.h>   
-#include <iostream>
-
-#include "Matrix.h" //definition of the class CMatrix
-#include "Structure3d.h"
-
-using namespace std;
-
-
-void help_display(){
-  cout<<"Help:"<<endl<<
-    "-f --> input trajectory file  (required) format .pdb"<<endl<<
-    //    "-n --> number of frames (default = 10000)"<<endl<<
-    //    "-beads --> beads to consider (default = [ C1' C2 P ] )"<<endl<<
-    "-of --> output file for fluctuations (DEFAULT = none)"<<endl<<
-    "-ribo --> is a riboswitch? (do I need to take away the last res because it's an ADA?) (default=false)"<<endl<<
-     "-h help"<<endl;;
-  return;
-}
-
-int main(int argc, char **argv){//PROGRAM MAIN
-  char file_name[200];
-  char oname[200];
-  bool out_has_name=false;
-  bool ribo=false;
-
-  cout<<" --- Program CompDist --- "<<endl<<endl;
-  cout<<" Computed the distance    "<<endl;
-  cout<<" fluctuations between C2 (or C6!!!!!!)  "<<endl;
-  cout<<" from a .pdb trajectory   "<<endl<<endl;
-  cout<<" ------------------------ "<<endl<<endl;
-  int i=1;
-  int nopar=0;
-  while(i<argc){
-    if(!strncmp(argv[i],"-f",2)){
-      i=i+1;
-      if(i>argc-1){cout<<"ERROR: empty parameter"<<endl; help_display(); return 0;}
-      sprintf(file_name,argv[i]);
-      nopar+=1;
-      cout<<"will analize the file "<<file_name<<endl;
-    }
-    else if(!strncmp(argv[i],"-of",3)){
-      i=i+1;
-      if(i>argc-1){cout<<"ERROR: empty parameter"<<endl; return 0;}
-      sprintf(oname,argv[i]);
-      cout<<"will write the flluctuations on the file "<<oname<<endl;
-      out_has_name=true;
-    }
-    else if(!strncmp(argv[i],"-ribo",5)){
-      cout<<" $ $ $ Riboswitch $ $ $ "<<endl;
-      ribo=true;
-    }
-
-    else if(!strncmp(argv[i],"-h",2)){
-      help_display();
-      return 0;
-    }
-    else{
-      cout<<"WARNING: input n. "<<i<<" "<<argv[i]<<" ---> invalid parameter"<<endl;
-    }
-    i=i+1;
-  }
-  if(nopar<1){cout<<"ERROR: insufficient number of parameters"<<endl;
-    help_display;
-    return 0;
-  }
-
-  if(!out_has_name)  sprintf(oname,"%s_C2_fluc.dat",file_name);
-  
-  double *dist_mean, *d_sq_mean;    
-  //  double *dist_mean, *d_sq_mean;    
-  Structure3d structure(0);
-  
-  //open input file
-  FILE* fin;
-  if ((fin = fopen (file_name, "r")) == NULL) {
-    fprintf (stderr,"CompDist:: Could not open file %s.\n.Exiting.\n", file_name);
-    exit (1);    }    
-  
-  //check if the input trajectory is correct
-  int error=0;
-  int Nsteps=0;
-  error=structure.readFromPDBFile(fin);
-  Structure3d ref_struc=structure;
-  int n_beads=structure.getSize();
-
-
-  int* is_C2=i1t(n_beads);
-  vector<int> indexC2;
-  for (size_t i = 0; i < ref_struc.getSize(); ++i){
-    if(ref_struc.getBead(i).getHet()) continue;
-    if ((ref_struc.getBead(i).getAtomType()=="C2") ||
-	(ref_struc.getBead(i).getAtomType()=="C6"))
-      {is_C2[i]=1; indexC2.push_back(i);}// cout<<"eccolo: "<<i<<endl;}
-  }
-  
-  cout<<"N. beads = "<<n_beads<<endl;
-
-  if(indexC2.size()<2) {cout<<"ERROR: INSUFFICIENT NUMBER OF C2 BEADS!!!"<<endl; return 0;}
-
-  vector<Vector3d> coords(indexC2.size());
-    
-  dist_mean=d1t(n_beads);
-  d_sq_mean=d1t(n_beads);
-  
-  cout<<"PrincipalComp: reading trajectory..."<<endl;
-  while(error==0){
-    ++Nsteps;
-    if(Nsteps%1000==0) cout<<"Frame: "<<Nsteps<<endl;
-
-     for (size_t i = 0; i < indexC2.size(); ++i){
-       int i_bead=indexC2.at(i);
-       coords[i] = structure.getBead(i_bead).getCoordinates();
-     }
-     //  $  $  $  $  $  $  $  $
-     
-    // #  #  #  #  #  #  # 
-     for (size_t i = 0; i < indexC2.size(); ++i){ //### qui calcolo le distanze
-       double temp_dsq=coords[i].distanceSQ(coords[i+1]);
-       d_sq_mean[i]+=temp_dsq;
-       dist_mean[i]+=sqrt(temp_dsq);
-     }
-    
-    error=structure.readFromPDBFile(fin);
-  }//end while
-
-  //close input file
-  fclose(fin);
-  cout<<"@@@ chiudo file input"<<endl;
-  cout<<"@@@ "<<Nsteps<<" frame letti."<<endl;
-
-  vector<double> fluct;
-  int n_C2=0;
-  if(ribo) n_C2=indexC2.size()-2;//NB: -2 per escludere ADA del riboswitch, altrimenti -1 !!
-  else n_C2=indexC2.size()-1;
-
-  for (size_t i = 0; i < n_C2; ++i){ 
-    d_sq_mean[i]/=Nsteps;
-    dist_mean[i]/=Nsteps;
-    fluct.push_back(d_sq_mean[i]-(dist_mean[i]*dist_mean[i]));
-  }
-  /// +++ OPEN the OUTPUT file +++
-  //  if(out_has_name){
-    ofstream fout;
-    fout.open(oname);
-    // ### qui calcolo le distanze e le printo ###
-    for (size_t i = 0; i < n_C2; ++i){ //NB: -2 per escludere ADA del riboswitch, altrimenti -1 !!
-      fout<<"X "<<i<<" "<<fluct.at(i)<<" "<<indexC2.at(i)<<" "<<ref_struc.getBead(indexC2.at(i)).getResName()<<endl;
-    }
-    fout.close();
-    //  }// +++ +++ +++ +++ +++ +++ +++  
-  
-  cout<<"...done!"<<endl<<endl;  
-  
-  return 0;
-
-}//END PROGRAM MAIN