[gmx-users] solvent density around protein

Matt Wyczalkowski matt.wyczalkowski at gmail.com
Mon Apr 6 17:50:02 CEST 2009

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.



2009/4/6 Morteza Khabiri <khabiri at greentech.cz>:
> 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 sense. Is it possible to compute the number
> of density with other commands of gromacs?
> Matt suggest me g_sorient but anyway it just give me total information
> about the solvent orientation like in box......The actual things that I
> want is that I want to know the density of water in each part of the
> protein.....
> I will be happy if you give me more suggestions.
> Before thanks
> Morteza
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