kay.gottschalk at weizmann.ac.il
Sat Jun 21 19:34:00 CEST 2003
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.
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
> might also rise to values >0.3nm after some nanoseconds
> 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
>> ~ 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!
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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
Herzl St. 1
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