[gmx-users] RMSD of MD run

[Ran Friedman]

I'm sorry - that was a typo. All vlaues should be in Angstroms.

Ran.

David van der Spoel wrote:

> On Thu, 2003-11-06 at 10:33, Ran Friedman wrote:
> > Hi,
> >
> > I've made a 3ns  md run of a system consisting a protein, a small
> > ligand, water and some salt molecules.
> > The backbone RMSD of the protein was stable during the first 2ns, with
> > a maximum value of 1.8nm. Most of the time the RMSD was ~1.5nm.
> > After ~2ns, the RMSD started rising. It reached ~1.95ns at 3ns.
>
> > My question is:
> > 1. Does this necessarily means that there's something wrong with my
> > simulation?
> > 2. If it doesn't, how can I verify it (i.e. how can I make sure that
> > the protein undergoes a some kind of a conformational change)?
> >
>
> Are you sure it's 1.5 nm? That sounds ridiculously high. Otherwise I've
> seen conformational changes happen after 50 ns, so anything is
> possible...
>
> > I'd appreciate any help,
> > Ran.
> > --
> > ------------------------------------------------------
> > Ran Friedman
> > Laser laboratory for fast reactions in biology
> > Department of biochemistry
> > Faculty of life sciences
> > Tel-Aviv university
> > 972-3-6409824
> > ------------------------------------------------------
> >
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org  http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> 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.

--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20031106/6d01fe8a/attachment.html>