VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Nov 03 2009 - 15:59:54 CST

Leonardo,
i am confused. Are the masses taken into account when "measure rgyr"
is used. i thought all the weights are equal and the formula
simplifies to:
rgyr := sqrt[ sum {(r_i -r_cm)^2} / N ]

what does "measure rgyr weight" compute then?

http://ftp.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node121.html

On Tue, Nov 3, 2009 at 5:13 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:
> On Tue, Nov 3, 2009 at 3:08 PM, Bernardo Sosa Padilla Araujo
> <bernardospa_at_gmail.com> wrote:
>> Hi all,
>>
>> can anyone tell me what the units are for the radius of gyration when using
>> the command "measure rgyr". Is it (A*A) or A?
>> In other terms, is it the square of Rg or just Rg?
>
> Rg is a radius, thus given in Angstroms. From the VMD source code, the
> definition is:
> rgyr := sqrt(sum (mass(n) ( r(n) - r(com) )^2)/sum(mass(n)))
>
> Cheers,
> Leo
>
>> Thanks a lot,
>>
>> Bernardo
>
>
>
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
> 

-- 
Roman Petrenko
Physics Department
University of Cincinnati