Hi Dina, The radius of gyration is defined as sqrt( (1/N) tr X'(I-jj')X ), which is the RMSD w.r.t. to the center of mass. It's the same thing. But I was talking about the tools g_gyrate and g_rms. The latter fits the structure to the reference structure and then sums the distances between paired atoms. That only works if you have a reference with all coordinates set to (0,0,0). But then the answer will be identical to that of g_gyrate, so why bother? Use g_gyrate, because it does what you want.
Cheers, Tsjerk On Sun, Jan 29, 2012 at 8:07 PM, dina dusti <[email protected]> wrote: > Hello Tsjerk, > > Thank you from your reply, but in the many papers, radius of micelle has > been obtained from both of them (i.e. gyration and root-mean-square distance > from center of mass of micelle). I don't know that how should I compute the > radius of a spherical micelle from rms distance of the headgroup atoms from > the micelle center of mass. > May I ask you to help me? > > Best Regards > Dina > > ________________________________ > From: Tsjerk Wassenaar <[email protected]> > To: dina dusti <[email protected]>; Discussion list for GROMACS users > <[email protected]> > Sent: Sunday, January 29, 2012 2:02 PM > Subject: Re: [gmx-users] root-mean-square distance > > Hi Dina, > > g_rms calculates the RMS from pairwise distances after performing a > least-squares fit. That's quite different from what you want, and > actually is what you get from g_gyrate... > > Cheers, > > Tsjerk > > On Sun, Jan 29, 2012 at 8:09 AM, dina dusti <[email protected]> wrote: >> Dear Specialists, >> >> I have a problem about computing of radius of micelle by >> root-mean-square-distance. Please help me. >> I obtained radius of my micelle 2.4 nm by g_gyrate. >> g_gyrate -f md.xtc -s md.tpr -o gyrate.xvg -b 150000 >> I want compare it by rms distance. >> I use from g_rms as following: >> g_rms -f md.xtc -s md.tpr -o distrmsd.xvg -n index.ndx -b 150000 >> It result me 3.992290e+00 nm after averaging by g_analyze -f distrmsd.xvg >> -av >> (the radius of a spherical micelle is defined as the rms distance of the >> headgroup atoms from the micelle center of mass, how should I define com >> of >> micelle in g_rms?) >> I think I am wrong somewhere. >> May I ask you to help me,Please? >> >> Best Regards >> Dina >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
