[gmx-users] g_spatial and vmd volume slice

Chris Neale chris.neale at utoronto.ca
Tue Feb 17 20:27:03 CET 2009

Dear Xavier,

"I have played with this recently and could not find the way to set or  
change the colors on the volume

see my previous post about how to do this with black/white and gimp/photoshop

"Moreover I found that the  
colors, although clearly showing the
expected pattern for the data plotted, it was also having strange  
behavior: it was giving a color to
certain regions that was not representative of the values."

Could you please elaborate? This is distressing. I do know that there is averaging between 4 boxes to create a value at the common vertex, but are you suggesting something even more problematic? I have never looked into the quantitative behaviour of the VMD volume slice option since it appears qualitatively correct to me.


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