[gmx-users] g_spatial and vmd volume slice

XAvier Periole x.periole at rug.nl
Wed Feb 18 13:36:25 CET 2009

> "I have played with this recently and could not find the way to set  
> or  change the colors on the volume
> slice."
> see my previous post about how to do this with black/white and gimp/ 
> photoshop
I did not find any mention of this in your previous post. But it is ok.
> "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.
It is not really easy to explain with words. Showing would have been  
Anyways I plot a property of a bilayer system: this property is high  
in the tail region, low in the
head groups region, and medium in the solvent.
With the volumeslice it looks like. averything is fine except in the  
head group region which is
shown low on the slice but in the "middle" of the head region is get  
the same color than the
tail region (representative of high values).

Note that I do not give volume map to VMD but I build it with it from  
raw data. That might be the
problem. I've not been looking further. The only thing sure is that I  
have no control of the
colors on the slice in this way. I may need to create an new  
representation after changing the
color scale.


> Chris.
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