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

[David van der Spoel]

On 2010-08-16 20.15, Chih-Ying Lin wrote:
>
>
> 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)

Yes, if you do not divide by the total mass you have the moments of 
inertia. Does this difference in definition explain it?


> 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  ?
No, it depends on the conformation.

>      => 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
>>
>
>
>


-- 
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