[gmx-users] Isovalue for g_spatial representation

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Oct 30 01:53:38 CEST 2010


I wrote g_spatial.

If you use the -nodiv option, then the iso-value represents the number  
of counts in that bin over the entire trajectory divided by the number  
of frames. Therefore the units would be "atomic occupancy counts per  
frame". Note that, as for all such histograms, the values of isolines  
and isosurfaces are dependent on bin size.

If you use the -div option (default), then the counts (already divided  
by the number of frames) are further divided by the number of atoms in  
the selection and then multiplied by the number of cells (similar to  
dividing by the volume of each cell). It's really a lot like an RDF: a  
number density per grid divided by the overall system density. It is,  
however, related to this by some multiplicative constant. You can find  
that because at the end of a g_density -div run, you will get an  
output of exactly what this divisor was, so you can go in using awk or  
whatever you like and modify the values as you see fit, turning values  
into proper densities if you like. Alternatively, you can run -nodiv  
and then divide all the the values yourself to get a proper density.


-- original message --

Hello gmx-users.
I calculated the spatial distribution functions for my solvent-solute
However I am in doubt in relation to the isovalue to be used in VMD to
the representation of the surface. The isovalue is admensional number or has
some unit?
There is some special criterium to choose its value?
Thank you in advance.

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