Hi, Does anyone know what the units of density are in the output (Gaussian 98 cube format) of the spatial distribution function in g_spatial? Is it a number density or a mass density? If it is a number density, then I would guess that the units might be atoms/nm^3, since nm is the unit of length in Gromacs. If it is a mass density, then I would guess that the units might be (atomic mass unit)/nm^3.
When I look in gmx_spatial.c, I see a line with the declaration "static const double bohr=0.529177249; /* conversion factor to compensate for VMD plugin conversion... */" [line 55]. It seems that this value is in the denominator in subsequent calculations [for example, lines 267-270]. I am not sure what this means. The comment in the code seems to imply that VMD does it own processing of the cube file. But when I asked on the VMD mailing list, I got this response: "The units are whatever the units of the data you loaded were. The values in the isovalue slider correspond directly to the data values that the associated VMD molfile plugin read from the input file, unless some kind of unit conversion was done on the fly, but in the case of volumetric data, none of the existing plugins do any unit conversions... The reason the units aren't specified is that many of the existing volumetric file formats don't include any provision to label the units in the file, and/or the programs that generate the volumetric files don't bother to write the units even if the file format supports it. The units of the isovalue slider in VMD are therefore directly related to the per-voxel scalar values stored in the volumetric data file, e.g. a density value (not the cartesian coordinates, not lengths, etc)." Indeed, when I open a cube file that is output by g_spatial, I do not see any units specified in the file (probably Gaussian98 does not support it). Do you have any suggestions? Thank you! Andrew DeYoung Carnegie Mellon University -- 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
