spoel at xray.bmc.uu.se
Sat Jun 21 20:01:01 CEST 2003
On Sun, 2003-06-22 at 05:32, Kay Gottschalk wrote:
> Danke fuer die schnelle Antowrt! I have 430 residues in a 2-domain
> protein, and just looking at it it looks o.k., actually. Nothing is
> exploding and the secondary structure elements seem to be conserved. T
> is 300 K.
If you have a two domain protein you may consider computing RMSD for the
individual domains too. They may be lower.
Furthermore, the larger the molecule the longer the equilbration time.
> On Saturday, June 21, 2003, at 10:24 AM, Rainer Boeckmann wrote:
> > - 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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> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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