[gmx-users] density of confined water

Sanku M msanku65 at yahoo.com
Tue Nov 29 17:48:43 CET 2011

  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.

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