[gmx-users] RMSD

[Rainer Boeckmann]

- the rmsd depends very much on your system size (how many residues do you have?
is it globular protein? T=?), see other comments in the list

- your system is almost certain not equilibrated after only 15ps. the rmsd-value
might also rise to values >0.3nm after some nanoseconds

cheers,
rainer

Kay Gottschalk wrote:

> Hi there,
>
> I am doing a free md of protein in water with ions, using the GROMOS96
> FF with pressure and T- coupling and PME for electrostatics. I
> positioned the ions with genion -random, as I read in the mailing list
> that the positioning using the best potential is screwed up. Is that
> so? The system equilibrates after 10-15 ps, but with a backbone RMSD of
> ~ 0.1 nm to the original structure. Coming from NMR, that seems rather
> high for me. Is this RMSd normal for free MD or do I have a problem?
> What kind of problem might I have (like: start structure not good or
> ions wrongly positioned)? Thanks for your help!
> Kay.
>
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--
Dr. Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

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