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Hi,<br>
<br>
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.<br>
<br>
Thank you <br>
<br>
Tom Piggot<br>
<br>
-------- Original Message --------
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<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Subject: </th>
<td>lateral diffusion coefficients on a spherical surface</td>
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<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Date: </th>
<td>Thu, 2 Dec 2010 08:05:36 +0000</td>
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<th nowrap="nowrap" valign="BASELINE" align="RIGHT">From: </th>
<td>Daniel <a class="moz-txt-link-rfc2396E" href="mailto:dah1g09@soton.ac.uk"><dah1g09@soton.ac.uk></a></td>
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<th nowrap="nowrap" valign="BASELINE" align="RIGHT">To: </th>
<td>Piggot T. <a class="moz-txt-link-rfc2396E" href="mailto:T.Piggot@soton.ac.uk"><T.Piggot@soton.ac.uk></a></td>
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<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">Dear Gromacs users,<br>
<br>
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.<br>
<br>
Firstly, I would like to calculate the arc length – the approximate
displacement across the surface of the sphere, instead of the linear
displacement. <br>
<br>
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?<br>
<br>
Thank you very much for your help,<br>
<br>
Daniel <br>
</span></font> <br>
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