Not R_x, R_y, and R_z. What I want to obtain are the three three principal moments of the ellipsoidal macromolecule.
They are different quantities. 2011/5/10 Erik Marklund <er...@xray.bmc.uu.se> > Mark Abraham skrev 2011-05-10 12.31: > > On 10/05/2011 8:23 PM, lammps lammps wrote: >> >>> Hi, >>> I want to study the shape change of a macromolecule which seems like a >>> ellipsoid. So, I need obtain the three principal moments of the molecules. >>> Is the command of g_gyrate helpful for me? The sum of the three principal >>> moments should be equal to the <Rg^2>. However, I used the command g_gyrate >>> -f traj.gro -s nvt.tpr -n anly.ndx -o shape.xvg -p obtain the Rg and other >>> three qualities. >>> It seems that the sum of the last three qualities is not equal to the >>> Rg^2. Is there something wrong? >>> >> >> Why should that sum equal Rg^2? >> >> Mark >> > Shouldn't it be half of that sum? > > Rg^2 = 1/N Sum([r_k - <r>]^2), > > where r are vectors and masses are set to unity for conveniance. If > decomposed in orthonormal axes x, y, and z, it yealds > > Rg^2 = 1/N Sum([x_k-<x>]^2 + [y_k-<y>]^2 + [z_k-<z>]^2). > > The radius of gyration around e.g. the x-axis is > > Rg_x^2 = !/N Sum([y_k-<y>]^2 + [z_k-<z_k>]^2). > > Hence Rg^2 = (Rg_x^2+Rg_y^2+Rg_z^2) / 2. > > That matches the numbers I get from my tests. > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://folding.bmc.uu.se/ > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- wade
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