VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 03 2009 - 16:32:20 CST

Roman,
  Yes, if you don't specify a per-atom field to use for the weight,
or an explicit weight list, then all atoms are assigned a weight of 1.0.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 03, 2009 at 06:18:24PM -0400, Roman Petrenko wrote:
> 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 

-- 
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