eef, 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.
Chris. -- original message -- Hello gmx-users. I calculated the spatial distribution functions for my solvent-solute system. However I am in doubt in relation to the isovalue to be used in VMD to control 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. eef -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
