Hi Chris, Druz
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
------------------------------
Message: 6
Date: Sat, 26 Nov 2011 10:17:10 -0500
From: chris.ne...@utoronto.ca
Subject: [gmx-users] diffusion of the water at the micelle surface
To: gmx-users@gromacs.org
Message-ID: <20111126101710.bbl5wl376s04c...@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
Stephane
------------------------------
Message: 7
Date: Sat, 26 Nov 2011 23:22:59 +0800
From: lina <lina.lastn...@gmail.com>
Subject: Re: [gmx-users] diffusion of the water at the micelle surface
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<cag9cjmnxasa7nj+8cgkhavodvobluvzqqruqrcsxzs37m6z...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
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
>
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