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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Nov 26 16:17:10 CET 2011

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.


-- 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


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