MD simulation analysis TSD Journal

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General

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.

Trajectories

PNGs were created with createTrajectories.pml and then combined into an animation with createAnim.sh.

Thermodynamics

Averages were calculated with R's "summary" function on grep-truncated xvg files.

Ramachandran plots

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

Additionally the data for the background distribution was downloaded from [1].
Then the scipt [2] was called.

B-Factor

Plots for comparing B-Factor based on all atoms and only C-alpha atoms were created with plotBFactors.pml.

Significance calculation

The p-value was computed with the script statTD.pl.