Hi,
For the ellipsoid model, my experience is that ~15 rounds of
optimisation are required. I can't reinforce enough how complex the
model-free combined optimisation and model selection problem actually
is (all explained in d'Auvergne E. J., Gooley P. R. (2007). Set theory
formulation of the model-free problem and the diffusion seeded
model-free paradigm. Mol. Biosyst., 3(7), 483-494.
http://dx.doi.org/10.1039/b702202f)! This can take up to 2 weeks
depending on how fast your computer is (at 2.4 GHz, I would expect 2
weeks). Note that later iterations are much faster than the start. I
haven't tested the convergence of the global model with simplex
optimisation, so I have no idea how long this will take and if
convergence can always be reached. One issue that can occur is a 3 to
4 iteration cycle around the universal solution (combined optimisation
minimum and model selection minimum, see the ref). This you can
manually check in the results files to see if any 2 are identical. If
so, you can stop the calculation. Any of the positions in the cycle
should be ok, as the models and values should be very similar for all
members. I really should add this check to the script! I hope this
helps,
Regards,
Edward
2010/5/5 Daniel Pérez <daniel.perez@xxxxxxxxxxxxxxxx>:
Hi everyone,
I've been running a full_analysis script with relaxation data at two fields
(600 and 900MHz). The calculations with models I to IV run successfully.
However, the ellipsoid model does not converge even after 7 rounds and more
than one week of calculation time.
I checked the mailing list and found one similar situation that happened to
Sebastien (October 24, 2007. Vol.17 issue 8 ... Extremely long optimization
times). I followed the suggestion by Edward in order to change the
minimization protocol from "newton" to "simplex". The result is that after
two weeks and 27 rounds the model ellipsoid still does not converge, and
with each next round the minimization becomes slower and slower.
The protein is an homodimer of 36KDa. For the model free analysis I'm using
the pdb structure of the monomer (18KDa), and I might have wrong assigned
resonances.
I'm running relax 1.3.4 on 2 cores Intel(R) Core(TM)2 CPU, 6600 @ 2.4GHz,
4M cache, and 4G ram.
Do you have any idea?. I'll appreciate any suggestion to follow with the
analysis.
Thanks
Daniel
Dr. Daniel Pérez
Institut für Molekularbiologie und Biophysik
Schafmattstrasse 20
ETH-Hönggerberg, HPK G 5
CH-8093 Zürich
Phone: +41 44 633 25 37
E-mail: daniel.perez@xxxxxxxxxxxxxxxx
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Re: Ellipsoid minimization does not converge