[gmx-users] g_gyrate

Dmitriy Golubobsky dmitriy.golubovsky at gmail.com
Fri Jan 26 09:54:29 CET 2007

Dear Gurus,
I've got question on Radius of gyrtion calculation.
my system consists of 1 polymer and a solvent.
I did MD and decide to calculate Rg for this system
I made index group consisting my residues
g_gyrate -f xtc_file -s tpr_file -n ndx_file -p -o xvg_output
ok. I've got the output file with 4 colums: time Rg Rx Ry Rz
I use -p option to get components in principal axes, because I' d like to
calculate form-factors for my system.

as I undersand Rg = sqrt ( sum_{i}^{N} r_i*m_i)/M)
ok. then fx=Rx/Rg^2, fy=Ry/Rg^2, fz=Rz/Rg^2
and I  wish to get fx+fy+fz=1 but it is not so.
where I'm mistaken?
How does components Rxyz in principal axes are calculated?
I'm using gromacs 3.3.1
Thanks a lot.

Dmitriy Golubovsky
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