[gmx-users] Is 2D projection

[Berk Hess]

Indeed.

I can add that an RMSD vs time plot tells you very little.
For proteins the RMSD from the starting structure will
quickly become constant, whereas a lot could still be happening.
An RMSD matrix gives you much more information:
g_rms -m


>From: Alan Dodd <anoddlad at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Is 2D projection  Date: Fri, 7 Jul 2006 00:10:49 
>-0700 (PDT)
>
>If you are referring to the output of g_anaeig, then
>the answer is yes.  It's rarely conclusive, of course,
>but it give you a good idea of how your simulation is
>sampling space.  A good plot would show lots of
>variation, whereas a bad plot would show a general
>drift.
>
>Alan.
>
>
>--- Wei Fu <fuwei at adrik.bchs.uh.edu> wrote:
>
> > Dear gmx users,
> >
> > Does the 2D projection plot has something to do with
> > convergence of the
> > trajectory? If so, what kind of shape of plot shows
> > the trajectory is
> > non-converged?
> >
> > Normally, I use RMSD plot to see if the trajectory
> > tends to converge. Now
> > my concern is how to see whether trajectory is
> > conserved or not based on
> > 2D projection analyses.
> >
> > Thanks in advance,
> >
> > Linda
> >
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