[gmx-users] g_gyrate

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 26 10:02:01 CET 2007

Dmitriy Golubobsky wrote:
> 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.
Rg = sqrt ( sum_{i}^{N} (r_i^2)*m_i)/M)

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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