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 <khab...@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 > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
