[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?
David van der Spoel
spoel at xray.bmc.uu.se
Mon Aug 16 20:26:40 CEST 2010
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
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