[gmx-users] solvent density around protein

First thanks Matt to reply me for my problem. As I say I want to calculate the density of solvent around protein. I already tried the commands g_density and g_densmap The g_density Compute partial densities across the box and g_densmap just give me one black and white photo which don't have

Re: [gmx-users] solvent density around protein

g_sorient spits out, at the end, among other things, the average number of solvent molecules within the cutoff distance. To get the number of e.g. water oxygens within a given distance of a group of atoms on a per frame basis, you can use g_hbond -contact. Best, Matt 2009/4/6 Morteza Khabiri