[gmx-users] diffusion of the water at the micelle surface

[lina]

On Sat, Nov 26, 2011 at 11:17 PM,  <chris.neale at 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
>
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