[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?

[David van der Spoel]

On 2010-08-14 23.49, Chih-Ying Lin wrote:
>
>
>
> Hi
> To Calculate the radii of gyration about the principal axes
>
> I use the command
> g_gyrate -p
>
> For lysozyme ,   I got  =>
> 0.922754     1.22249     1.25603
>
> but in some paper, the authors got
> => 0.660  0.833  0.991
>
> It is a quite difference.
>
> what is the definition of the radii of gyration about the principal axes  ?
> i have checked the Gromacs manual but see nothing there.

The difference seems to be a constant factor.
Gromacs computes
sqrt (sum m (r-r_com)^2 / sum m)
I'm pretty sure it says so in the manual.


>
>
> Thank you
>
> Lin
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se