[gmx-users] density of confined water

[Sanku M]

Hi,
  I would like to know if there is a way in gromacs to calculate the time-averaged density of solvent which is confined between two objects , say, two plates or another example will be water confined between ligand and binding-pocket.
I was thinking about two ways for going about this but in both cases there are some issues:
1. I found there is a tool g_densmap but it gives a 2D density map. But, in this case, I guess, 3D map would have been necessary.

 2. Also, I found trjorder with -nshell option can calculate number of waters within a distance (with -r option) . But, in this case, I need to know volume of the confined space as well. I am not sure gromacs can calculate the volume of the confined space.

Any help or suggestion of  any other suitable  methods will be highly appreciated.

Sanku
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111129/973fbadc/attachment.html>