\(\(f1[molecule_] := 
        Module[
{infile, points, logpts, i, 
            x}, 

Run["perl $LABPATH/1/1.pl", \(( .001\ *\ Sqrt[3])\), 
            molecule]; 

points = 
            ReadList["$LABTMP/1", \ {Number, 
                Number}]; 

logpts = {}; 
For[i = 1, 
            i ≤ \(Dimensions[
                  points]\)[\([1]\)], \(i++\), 
\(logpts = 
                Append[logpts, {points[\([i, 1]\)], 
                    Log[2, points[\([i, 
                          2]\)]]}];\)
]; 
linfit = 
            Fit[logpts, {1, x}, {x}]; 
ListPlot[points, 
            PlotJoined -> True, 
            PlotLabel -> "Ratio of RMSD to initial RMSD", 
            PlotStyle -> RGBColor[0, 0, 1]]; 
Show[
            ListPlot[logpts, PlotStyle -> RGBColor[0, 0, 1], 
              DisplayFunction -> Identity], 
            Plot[linfit, {x, 0, 200}, PlotStyle -> RGBColor[1, 0, 0], 
              DisplayFunction -> Identity], 
            PlotLabel -> "Log base 2 of above", 
            DisplayFunction -> $DisplayFunction];
];\)\)

(* 
      initial RMSD is 0.001732 *) 

molecule  =  1;
 (* 
      molecules are : 
1  -  waters,  
      2  -  decalanine,  
      3  -  alanine dipeptide
*) 


    f1[molecule]