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 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]> 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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