VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 03 2009 - 16:13:10 CST

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
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