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I calculated a gaussian scan job for propylcyclohexane with two dihedral angles. Now I want to display a potential energy surface for that molecule with molden. I am new to molden and only found the geom. convergence button so far. This creates an two dimensional plot, but I need a three dimensional surface, with the energy plotted against the two dihedral angle changes. Is there a way to do this in molden?

This in my input file for the calculation:

%cpu=16-31
%mem=32GB
%chk=propylcyclohexan_scan_10.chk
#p PM6 Opt=modredundant

 propylcyclohexan_scan_10

0 1
C         -2.32729        0.36923       -0.26826
C         -1.86086        1.79592        0.04793
C         -1.42371       -0.68619        0.35867
H         -2.35296        0.22494       -1.35567
H         -3.35311        0.22391        0.09146
C         -0.38557        2.05033       -0.34666
H         -1.99132        1.97106        1.12477
H         -2.51564        2.50378       -0.47169
C          0.03534       -0.45199       -0.00958
H         -1.73512       -1.68573        0.02974
H         -1.53451       -0.66689        1.44998
C          0.49676        0.97326        0.33008
H          0.17109       -0.63513       -1.08350
H          0.66387       -1.18248        0.51357
H          0.48096        1.10355        1.41947
H          1.53881        1.06369        0.01138
C          0.03241        3.54672       -0.05839
H         -0.30194        1.90196       -1.43267
C          1.54273        3.82216       -0.15556
H         -0.26571        3.76488        0.97694
H         -0.55219        4.21744       -0.69950
C          2.23970        5.10589       -0.65389
H          2.00099        3.01727       -0.72714
H          1.90136        3.75452        0.88334
H          2.45381        5.07336       -1.75369
H          3.23327        4.96387       -0.25958
H          2.02974        6.11114       -0.31960

D 6 17 19 22 S 35 10.0
D 12 6 17 19 S 35 10.0
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  • 3
    $\begingroup$ I am not aware that molden is capable of plotting potential energy surfaces (PES). This is not what molden is primarily made for. Instead you can extract the PES as a table from the gaussian output file and then use any general plotting software (e.g. gnuplot or Python/matplotlib) to display it. The "geom. convergence" feature is intended to show how a geometry optimization converges over its iterations. This is something completely different from a PES. $\endgroup$
    – Feodoran
    May 21, 2020 at 11:29
  • 1
    $\begingroup$ Chemcraft might be able to do it out of the box, but it's not free. I'm not sure if Avogadro can do it; it's worth checking though. Otherwise plotting it should work quite well, obviously you lose the ability to view the structure interactively. $\endgroup$ May 21, 2020 at 13:20
  • 3
    $\begingroup$ This question might fit better on the new Materials Modeling SE, as it is more of a software issue than a chemical problem. $\endgroup$
    – Tyberius
    May 21, 2020 at 14:42

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