VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Nov 03 2009 - 16:18:24 CST

John,
thanks for reply. So, if one uses
measure rgyr [atomselect top protein]
then masses are _not_ taken into account, right?

On Tue, Nov 3, 2009 at 6:13 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Roman,
>  The "weight" parameter will cause the positions to be weighted by
> whatever per-atom weight parameter you choose, normally "mass".
> This is similar to the various other measure commands that accept
> a user-defined weighting parameter.
>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Tue, Nov 03, 2009 at 05:59:54PM -0400, Roman Petrenko wrote:
>> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> 

-- 
Roman Petrenko
Physics Department
University of Cincinnati