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 .
Thank you for your response
Stephane
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