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: [email protected] > > To: [email protected] > > 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: [email protected] > > cell: 206-850-7468 > > skype=aroberts92122 > > > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------------------------------------------------------ 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: [email protected] Skype: ran.friedman ------------------------------------------------------
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