Hi,
I am forwarding on a message on behalf of one of my colleagues who is
having problems sending messages to the list. Please take a look his
message and see if you can help him with his problem.
Thank you
Tom Piggot
-------- Original Message --------
Subject: lateral diffusion coefficients on a spherical surface
Date: Thu, 2 Dec 2010 08:05:36 +0000
From: Daniel <[email protected]>
To: Piggot T. <[email protected]>
Dear Gromacs users,
I would like to calculate some lateral diffusion coefficients of
molecules on a spherical surface. I realise that there is no gromacs
tool that can do this, but I was wondering if there might be a clever
way to edit the code for g_msd? I am currently using Gromacs version 4.0.7.
Firstly, I would like to calculate the arc length – the approximate
displacement across the surface of the sphere, instead of the linear
displacement.
Secondly, I would like to remove any angular movement resulting from the
rotation of the whole sphere. I realise that there may be a way to do
this during the simulation using the com_mode set to angular, but is
there a way to post process a trajectory to remove the rotation of the
whole sphere? Would post processing of the simulation trajectory
introduce errors?
Thank you very much for your help,
Daniel
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