Sunday, April 28, 2019

computational chemistry - Software for visualizing molecular force vectors


I would like to visualize molecular normal modes as vectors sitting on each atom, and not as actual vibrations. I am able to do this, in part, with Molden by copying in the vector into a file readable by Molden (extension is .geo.molden, and is generated from a Molcas calculation). The vector is represented as red lines, but they do not look very nice (see image). Also the background is black, and Molden has a limited number of ways to visualize the molecule.


Is there some other software (free) that can do this? Perhaps Avogadro, VMD, or something along these lines? Specifically I would like to be able to change to different molecular visualizations, and show the vectors as arrows with a easily distinguished color.


enter image description here Figure 1. This is what Molden can do... not very pretty!



Or possibly, after changing the background color to white with GIMP:


enter image description here Figure 2. Not really better, since the Hydrogen atoms are represented with white by Molden, as is the label text.




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