[gmx-users] Is 2D projection
gmx3 at hotmail.com
Fri Jul 7 09:33:03 CEST 2006
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:
>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
>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
>--- 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
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> > list. Use the
> > www interface or send it to
> > gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
>Do You Yahoo!?
>Tired of spam? Yahoo! Mail has the best spam protection around
>gmx-users mailing list gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users