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Plot a free energy landscape?

Posted 1 month ago
4 Replies
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Most times I get the correct rainbow colors of the Gibbs free energies. But some data is giving me a different image. I don't know what to change.

please, I very new to Mathematica.

I have attached the following: The .nb file I am using. The image I'm getting (amber12_23) The image I expect (FEL) the data (amber12_23.txt)

Any help will be appreciated.

4 Replies

Hi Lucy,

if I execute you code I do get the desired/expected result (i.e. similar to FEL.tiff). Maybe you need to make a clean start (e.g. by executing ClearAll["Global`*"] at the beginning of you notebook). And the PlotRange option is not really needed.

Regards -- Henrik

Thank you Henrik. But it has refused to work. I have even "quit the kernel" to completely refresh but it's not working. Maybe could be the version of the Mathematica? I'm using 10.2

Well, strange, I do not have any idea of what the problem could be here. I was trying this successfully on v11.3 and v12.0. Instead of using ListContourPlot: Does probably ContourPlot work for you?, e.g.

fel = Interpolation[{{#1, #2}, #3} & @@@ arrayData];
ContourPlot[fel[\[FormalX], \[FormalY]], 
 Evaluate[Sequence @@ 
   MapThread[Prepend, {First[fel], {\[FormalX], \[FormalY]}}]], 
 ColorFunction -> ColorData["Rainbow"], ContourStyle -> None, 
 FrameLabel -> {"PC2", "PC3"}, GridLines -> Automatic, 
 LabelStyle -> {FontSize -> 20, FontFamily -> "Times", Black, Bold},
 PlotRange -> All, 
 FrameTicks -> {{{0.4, 0.6, 0.8, 1.0, 1.2, 1.4}, 
    None}, {{0.4, 0.6, 0.8, 1.0, 1.2, 1.4}, None}}, 
 PlotLabel -> Style["FEL: Amber/Tip4p-eW", FontSize -> 18], 
 PlotLegends -> 
  BarLegend[All, LegendLabel -> "kJ/mol", 
   LabelStyle -> {Bold, Black, "Times", Bold[0.3], 18}]]


What happens when you use your original code with:

ListContourPlot[(*bla bla*), PlotRange->All]

Dear Henrik! I have used your code and it has worked!!!!

Also, PlotRange -> All, has worked fine with my code!

I'm grateful, Thank you so much!!

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