[gmx-users] RMSD

[David]

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.


> Cheers,
> Kay.
> 
> 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
> >
> > tel:    +49(551)201-1141
> > mobile: +49(172)9531168
> > fax:    +49(551)201-1089
> >
> > email: rboeckm at gwdg.de
> >
> > http://www.mpibpc.gwdg.de/abteilungen/071/rainer/index.html
> >
> >
> >
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> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Tel: ++972-8-9343639
> Herzl St. 1
> Rehovot 76100
> Israel
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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
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