[gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS?

[Ran Friedman]

Hi Art,

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.

Ran

Berk Hess wrote:
> Hi,
>
> There might be a way to do this with Gromacs.
> But I would think a protein is simply a volume (maybe with one
> attached water layer)
> for which there is a simple approximation for the hydrodynamic radius
> in hydrodynamics.
>
> Berk
>
> > From: aroberts99163 at yahoo.com
> > To: gmx-users at gromacs.org
> > Date: Wed, 18 Aug 2010 14:25:26 -0700
> > Subject: [gmx-users] Is there a way to calculate the hydrodynamic
> radius using GROMACS?
> >
> > Hi, all,
> >
> > I was curious, if there is a way to calculate the hydrodynamic radius
> > of a protein using GROMACS?
> >
> > Much appreciated,
> > Art
> >
> > Dr. Arthur Roberts, Ph.D.
> > University of California, San Diego
> > Skaggs School of Pharmacy and Pharmaceutical Sciences
> > 9500 Gilman Drive #0703
> > La Jolla, CA 92093-0703
> >
> > email: aroberts99163 at yahoo.com
> > cell: 206-850-7468
> > skype=aroberts92122
> >
> >
> >
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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: r.friedman at bioc.uzh.ch
Skype: ran.friedman
------------------------------------------------------

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