[gmx-users] RMSD

[Kay Gottschalk]

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.
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
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>
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>
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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