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

[chris.neale at utoronto.ca]

Well, the positive way of looking at this is that it appears that  
nobody has ever done it before. If somebody has done it (in charmm for  
instance) then you might be able to convert the format of your .xtc  
and use their tools to analyze it.

Good luck,
Chris.

-- original message --

Thank you very much for your reply. Indeed I have read several papers  
where the diffusion of water at the membrane surface have been  
computed. Since the diffusion of the interfacial water is an useful  
properties to examine the micelle/surface irregularities, I would hope  
that this option exist in gromacs. Unfortunately, it is not the case,  
so i will try your suggestions .

Stephane


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Message: 6
Date: Sat, 26 Nov 2011 10:17:10 -0500
From: chris.neale at utoronto.ca
Subject: [gmx-users] diffusion of the water at the micelle surface
To: gmx-users at gromacs.org
Message-ID: <20111126101710.bbl5wl376s04ccww at webmail.utoronto.ca>
Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
         format="flowed"

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