[gmx-users] Fwd: lateral diffusion coefficients on a spherical surface

[Thomas Piggot]

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 <dah1g09 at soton.ac.uk>
To: 	Piggot T. <T.Piggot at soton.ac.uk>



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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