Visual. Quickstart Guide

How to: scientific plots

xmgrace

A tutorial can be found here:
https://universe.bits-pilani.ac.in/uploads/Pilani/navin/ReadPDFDOC/xmgrace.pdf

gnuplot

A lot of example plots can be seen here (an example plot is also shown in the appendix):
http://gnuplot.sourceforge.net/demo/

Gnuplot template for pdf plots (resulting example plot shown below):

Code 
    #!/usr/bin/gnuplot
    reset
    # plot a pdf
    set terminal pdfcairo enhanced font "Times New Roman,12.0" rounded
    set output 'confinement_plot.pdf'
    set border linewidth 1.0
    set size ratio 0.55
    # set plot line styles
    set style line 1 linecolor rgb 'black'   linetype 1 linewidth 1
    set style line 2 linecolor rgb '#FFB85F' linetype 1 linewidth 1   #yellow
    # set legend position
    set key left top
    # set axis properties
    set ylabel 'V(r)'
    set xlabel 'r / Bohr'
    set xtics nomirror
    set ytics nomirror
    set xr[0:10]
    set yr[0:9]
    #variables
    w = 8.5
    r0 = 4.0
    a = 2.0
    r1=2.5
    #functions
    f (x) = w / ( 1 + exp (a * (r0 - x)))
    g (x) = (x/r1)**2
    # plot funcitons
    plot  f(x)  title 'Wood-Saxon Confinement' w lines linestyle 1, \
              g(x)  title 'Power Confinement'      w lines linestyle 2

    ### for plotting data files:
    # plot "name_of_datafile.dat" w lines

gnuplot example plot

matplotlib

Quickstart guide:
https://matplotlib.org/stable/users/getting_started/index.html

julia

Found on the net (not testet yet, but seems useful):
https://nextjournal.com/leandromartinez98/tips-to-create-beautiful-publication-quality-plots-in-julia

How to: vmd eye candy

  • Set background color to white (a good .vmdrc file is shown in the appendix)

  • Adjust camera to a nice perspective of the molecule and set the resolution of atoms and bonds in graphical representations to 25

  • File -> Render ...

  • Select "Tachyon"

  • add to the the command before the -o flag "-res 3000 3000" so that i looks like "... TARGA -res 3000 3000 -o ..."

  • autocrop and scale the image to a smaller size it with gimp, done!

Good default VMD settings (stolen from Bernhard, copy content end save it in .vmdrc in your home directory):

Code 
    color Display Background white
    color Axes Labels black
    color Labels Bonds black
    color Labels Angles black
    display depthcue off
    ## position and turn on menus
    menu main move 5 225
    menu display move 395 30
    menu graphics move 395 500
    menu main on
    menu graphics on
    mol delrep 0 top
    mol representation Licorice 0.100000 12.000000 1.000000
    mol addrep top
    mol representation DynamicBonds 1.600000 0.100000 12.000000
    mol addrep top