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
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