[gmx-users] Re: gmx-users Digest, Vol 33, Issue 67

[Dmitriy Golubobsky]

>
> ---------- Пересланное письмо ----------
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Fri, 26 Jan 2007 10:02:01 +0100
> Subject: Re: [gmx-users] g_gyrate
> Dmitriy Golubobsky wrote:
> > Dear Gurus,
> > I've got question on Radius of gyrtion calculation.
> > my system consists of 1 polymer and a solvent.
> > I did MD and decide to calculate Rg for this system
> > I made index group consisting my residues
> > g_gyrate -f xtc_file -s tpr_file -n ndx_file -p -o xvg_output
> > ok. I've got the output file with 4 colums: time Rg Rx Ry Rz
> > I use -p option to get components in principal axes, because I' d like
> > to calculate form-factors for my system.
> >
> > as I undersand Rg = sqrt ( sum_{i}^{N} r_i*m_i)/M)
> > ok. then fx=Rx/Rg^2, fy=Ry/Rg^2, fz=Rz/Rg^2
> > and I  wish to get fx+fy+fz=1 but it is not so.
> > where I'm mistaken?
> > How does components Rxyz in principal axes are calculated?
> > I'm using gromacs 3.3.1
> > Thanks a lot.
> Rg = sqrt ( sum_{i}^{N} (r_i^2)*m_i)/M)
>
> --
> David.
>
> Dear David,
I understand this, thus for the
Rx=Rg = sqrt ( sum_{i}^{N} (x_i^2)*m_i)/M)

and we have to get Rx^2+Ry^2+Rz^2=Rg^2
but we didn't get this.
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