[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?
Chih-Ying Lin
chihying2008 at gmail.com
Mon Aug 16 20:15:54 CEST 2010
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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