On Sat, Nov 26, 2011 at 11:17 PM, <chris.ne...@utoronto.ca> wrote: > When people do this for lipid bilayers, they compute depth-dependent > diffusion profiles (often diffusion is computed separately for lateral > diffusion and diffusion along the bilayer normal). Sounds like you might do > something similar. I doubt that the standard gromacs tools will do this for > you. If you don't hear from anybody about how to do this, then I'd suggest > that you simply use g_dist to get the time-dependent distance for each water > molecule and then use g_traj to output the coordinates of each water > molecule and then script it yourself after reading one of the papers where > people compute depth-dependent diffusion profiles for a lipid bilayer. > > Chris. > > -- original message -- > > I would like to compute the translational diffusion around the micelle > surface. I know that I can select the water molecules at x distance of the > micelle surface with g_select (right ?) but how to use this file generated > by g_select to compute de diffusion, since the index and/or the number of > water will change with the simulation time .
You may try g_density, choose different time interval. > > > > Thank you for your response > > > > Stephane > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists