MD simulation analysis TSD Journal
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Most of the base data was calculated according to the tutorial with a slightly modified version of scripts by Hemochromatosis. These are calcData.pl, create.sh, xmgrace.sh for creating the plots and convert.sh to convert the plots to PNG.
Averages were calculated with R's "summary" function on grep-truncated xvg files.
At first the .xvg files were parsed into the following format:
ID Psi Phi Aa 1HMP:chain0:Pro5 -92.926842 12.941312 Proline 1HMP:chain0:Gly6 65.796807 -162.229709 Glycine 1HMP:chain0:Val7 -81.132082 121.413022 General
Plots for comparing B-Factor based on all atoms and only C-alpha atoms were created with plotBFactors.pml.
The p-value was computed with the script statTD.pl.