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Hi Art,<br>
<br>
For a globular protein, it should correlate with the gyration radius.
You can have a look at Dashevskaya et al., PROTOPLASMA 234: 13-23 for
some discussion about the relation of the radius of gyration and Stokes
radius. <br>
<br>
Ran<br>
<br>
Berk Hess wrote:
<blockquote cite="midCOL113-W39C638680F072B19BA6E868E9E0@phx.gbl"
type="cite">
<style><!--
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--></style>Hi,<br>
<br>
There might be a way to do this with Gromacs.<br>
But I would think a protein is simply a volume (maybe with one attached
water layer)<br>
for which there is a simple approximation for the hydrodynamic radius
in hydrodynamics.<br>
<br>
Berk<br>
<br>
> From: <a class="moz-txt-link-abbreviated" href="mailto:aroberts99163@yahoo.com">aroberts99163@yahoo.com</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Date: Wed, 18 Aug 2010 14:25:26 -0700<br>
> Subject: [gmx-users] Is there a way to calculate the hydrodynamic
radius using GROMACS?<br>
> <br>
> Hi, all,<br>
> <br>
> I was curious, if there is a way to calculate the hydrodynamic
radius <br>
> of a protein using GROMACS?<br>
> <br>
> Much appreciated,<br>
> Art<br>
> <br>
> Dr. Arthur Roberts, Ph.D.<br>
> University of California, San Diego<br>
> Skaggs School of Pharmacy and Pharmaceutical Sciences<br>
> 9500 Gilman Drive #0703<br>
> La Jolla, CA 92093-0703<br>
> <br>
> email: <a class="moz-txt-link-abbreviated" href="mailto:aroberts99163@yahoo.com">aroberts99163@yahoo.com</a><br>
> cell: 206-850-7468<br>
> skype=aroberts92122<br>
> <br>
> <br>
> <br>
> -- <br>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
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