VMD-L Mailing List

From: Lutz Maibaum (lutz.maibaum_at_gmail.com)
Date: Wed Jun 20 2007 - 20:35:15 CDT

Hello,

I was wondering if the documentation of the "volmap" command [1] contained
an error. I believe that instead of
  volmap <atom selection> <maptype>
it should be
  volmap <maptype> <atom selection>

Also, what is the default range for which the volumetric map is computed if
the -minmax option is not specified? I run into problems with the default
setting for my trajectories, where VMD has the correct unit cell
information (as shown by "pbc get"), but the volume used for the gridding
is larger than that:

vmd > pbc get
{86.177399 86.177399 86.177399 90.000000 90.000000 90.000000}
vmd > volmap density [atomselect top "all"] -res 1.0
volmap: Computing bounding box coordinates
volmap: grid minmax = {-11.000000 -11.000000 -11.000000} {97.000000
97.000000 97.000000}
volmap: grid size = 109x109x109 (4.9 MB)

I can use the -minmax option to restrict the range to the actual box size,
but I was wondering if there was a way to do this automatically.

Thanks,

  Lutz

[1] http://www.ks.uiuc.edu/Research/vmd/current/ug/node141.html#7633