\(\(\(f6[stepsize_] := 
        Module[
{infile, points, l1, l2, s1, s2, files, 
            titles, i}, 

files = {"$LABTMP/lts.mdx.alanin.err", "$LABTMP/sts.mdx.alanin.err", "$LABTMP/lts.mdx.water.err", "$LABTMP/sts.mdx.water.err"}; 
titles = {"Alanine Dipeptide Energy", "Alanine Dipeptide Shadow Energy", "Waters Energy", "Waters Shadow Energy"}; 

Run["/bin/sh $LABPATH/6/ss6.sh", \ 
            stepsize]; 

Print["Red is full timestep, Blue is half timestep"]; 

For[j = 1, 
            j ≤ 2, \(j++\), 
points = 
              ReadList[
                files[\([2  j - 1]\)], {Number, Number, Number, Number, 
                  Number, Number, Number}]; 
l1 = {}; 
            l2 = {}; 
For[i = 1, 
              i ≤ \(Dimensions[points]\)[\([1]\)], \(i++\), 
              l1 = Append[
                  l1, {stepsize*points[\([i, 1]\)], 
                    points[\([i, 2]\)]}]; 
l2 = 
                Append[l2, {stepsize*points[\([i, 1]\)], 
                    points[\([i, 
                        6]\)]}];
]; 
points = 
              ReadList[
                files[\([2  j]\)], {Number, Number, Number, Number, Number, 
                  Number, Number}]; 
s1 = {}; 
            s2 = {}; 
For[i = 1, 
              i ≤ \(Dimensions[points]\)[\([1]\)], \(i++\), 
              s1 = Append[
                  s1, {stepsize*points[\([i, 1]\)]/2, 
                    points[\([i, 2]\)]}]; 
s2 = 
                Append[s2, {stepsize*points[\([i, 1]\)]/2, 
                    points[\([i, 
                        6]\)]}];
]; 

Show[
              ListPlot[l1, PlotJoined -> True, 
                PlotStyle -> RGBColor[1, 0, 0], 
                DisplayFunction -> Identity], 
              ListPlot[s1, PlotJoined -> True, 
                PlotStyle -> RGBColor[0, 0, 1], 
                DisplayFunction -> Identity], 
              PlotLabel -> titles[\([2  j - 1]\)], 
              DisplayFunction -> $DisplayFunction]; 

Show[
              ListPlot[l2, PlotJoined -> True, 
                PlotStyle -> RGBColor[1, 0, 0], 
                DisplayFunction -> Identity], 
              ListPlot[s2, PlotJoined -> True, 
                PlotStyle -> RGBColor[0, 0, 1], 
                DisplayFunction -> Identity], 
              PlotLabel -> titles[\([2  j]\)], 
              DisplayFunction -> $DisplayFunction];
];
];\)\(
\)
    \)\)

stepsize = 2.0;
f6[stepsize]