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

[Chih-Ying Lin]

HI
What is the math definition of the radii of gyration about the principal
axes in Gromacs?

 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.

>From David =>
"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."


1. so the different factor is   sum m ,  not sum_N,   right ?  (N= number of
atoms)
2. the choice of the principal axes of the protein molecule is a standard
process ?
    => I mean the principal axes of the protein molecule  is fixed, right  ?
    => I mean the math of the principal axes of the protein molecule is
defined all over the world , right ?

Thank you
Lin






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
>
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