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
