[gmx-users] principal moments of ellipsoid

[Justin A. Lemkul]

lammps lammps wrote:
> Not R_x, R_y, and R_z.
>  
> What I want to obtain  are the three three principal moments of the 
> ellipsoidal macromolecule.
>  
> They are different quantities.
>  
> 

Then isn't g_principal the more appropriate tool, rather than g_gyrate?

-Justin

> 
>  
> 2011/5/10 Erik Marklund <erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>>
> 
>     Mark Abraham skrev 2011-05-10 12.31:
> 
>         On 10/05/2011 8:23 PM, lammps lammps wrote:
> 
>             Hi,
>             I want to study the shape change of a macromolecule which
>             seems like a ellipsoid.  So, I need obtain the three
>             principal moments of the molecules.
>             Is the command of g_gyrate helpful for me? The sum of the
>             three principal moments should be equal to the <Rg^2>.
>              However, I used the command g_gyrate -f traj.gro -s nvt.tpr
>             -n anly.ndx -o shape.xvg -p obtain the Rg and other three
>             qualities.
>             It seems that the sum of the last three qualities is not
>             equal to the Rg^2. Is there something wrong?
> 
> 
>         Why should that sum equal Rg^2?
> 
>         Mark
> 
>     Shouldn't it be half of that sum?
> 
>      Rg^2 = 1/N Sum([r_k - <r>]^2),
> 
>     where r are vectors and masses are set to unity for conveniance. If
>     decomposed in orthonormal axes x, y, and z, it yealds
> 
>      Rg^2 = 1/N Sum([x_k-<x>]^2 + [y_k-<y>]^2 + [z_k-<z>]^2).
> 
>     The radius of gyration around e.g. the x-axis is
> 
>      Rg_x^2 = !/N Sum([y_k-<y>]^2 + [z_k-<z_k>]^2).
> 
>     Hence Rg^2 = (Rg_x^2+Rg_y^2+Rg_z^2) / 2.
> 
>     That matches the numbers I get from my tests.
> 
>     -- 
>     -----------------------------------------------
>     Erik Marklund, PhD student
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,    75124 Uppsala, Sweden
>     phone:    +46 18 471 4537        fax: +46 18 511 755
>     erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>  
>      http://folding.bmc.uu.se/
> 
> 
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
> -- 
> wade
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================