Dear Troels and Edward,
Thank you for the pointers. I was not aware that a new version was out last
week, so I’ve asked the IT people to install it on our cluster. Below is the
output from ‘relax -i’:
[chungke@nmrc10 onc_dAUGA_MES_310K]$ relax -i
relax repository checkout r24533
svn://svn.gna.org/svn/relax/trunk
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2014 the relax development team
This is free software which you are welcome to modify and redistribute under
the conditions of the
GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL' within the
relax prompt.
Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
the prompt.
Processor fabric: Uni-processor.
Hardware information:
Machine: x86_64
Processor: x86_64
Processor name: Intel(R) Xeon(R) CPU E5430 @ 2.66GHz
Endianness: little
Total RAM size: 7983 Mb
Total swap size: 8189 Mb
Operating system information:
System: Linux
Release: 2.6.18-164.el5
Version: #1 SMP Thu Sep 3 03:28:30 EDT 2009
Distribution: redhat 5.3 Final
Full platform string: Linux-2.6.18-164.el5-x86_64-with-redhat-5.3-Final
Python information:
Architecture: 64bit ELF
Python version: 2.5.1
Python build: r251:54863, Jul 23 2008 17:35:20
Python compiler: GCC Intel(R) C++ gcc 4.1 mode
Libc version: glibc 2.3
Python executable: /program/nmr/bin/python
Python module path: ['/program/nmr/relax',
'/program/nmr/lib/python2.5/site-packages/setuptools-0.6c9-py2.5.egg',
'/program/nmr/lib/python25.zip', '/program/nmr/lib/python2.5',
'/program/nmr/lib/python2.5/plat-linux2',
'/program/nmr/lib/python2.5/lib-tk',
'/program/nmr/lib/python2.5/lib-dynload',
'/program/nmr/lib/python2.5/site-packages',
'/program/nmr/lib/python2.5/site-packages/Scientific/linux2']
Python packages and modules (most are optional):
Name Installed Version Path
minfx True 1.0.8
/program/nmr/lib/python2.5/site-packages/minfx
bmrblib True 1.0.3
/program/nmr/lib/python2.5/site-packages/bmrblib
numpy True 1.6.2
/program/nmr/lib/python2.5/site-packages/numpy
scipy False
wxPython False
matplotlib True 0.98.3
/program/nmr/lib/python2.5/site-packages/matplotlib
mpi4py True 1.3.1
/program/nmr/lib/python2.5/mpi4py
epydoc False
optparse True 1.5.3
/program/nmr/lib/python2.5/optparse.pyc
readline True
/program/nmr/lib/python2.5/lib-dynload/readline.so
profile True
/program/nmr/lib/python2.5/profile.pyc
bz2 True
/program/nmr/lib/python2.5/lib-dynload/bz2.so
gzip True
/program/nmr/lib/python2.5/gzip.pyc
io False
xml True 0.8.4 (internal)
/program/nmr/lib/python2.5/xml/__init__.pyc
xml.dom.minidom True
/program/nmr/lib/python2.5/xml/dom/minidom.pyc
relax information:
Version: repository checkout r24533
svn://svn.gna.org/svn/relax/trunk
Processor fabric: Uni-processor.
relax C modules:
Module Compiled File type
Path
target_functions.relax_fit True ELF 64-bit LSB shared object, AMD
x86-64, version 1 (SYSV), not stripped
/program/nmr/relax/target_functions/relax_fit.so
As for the data itself, I am using data obtained on two fields and use both
from the start.
Upon closer look at the R20 parameters, I think both of you are right: the
R20a and R20b numbers are really funky. I shall follow your suggestions and
run the calculations with the CR72 and B14 models instead.
Cheers,
Chung-ke
On Sep 9, 2014, at 4:25 PM, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
wrote:
Hi Chung-ke.
Can you put the information about which version of relax you use?
You can in terminal do:
relax -i
and write it here.
And then there is the question if you used data from one field or two
spectrometer fields.
Fitting to one field, can give problems.
This is described here:
"""Faithful estimation of dynamics parameters from CPMG relaxation
dispersion measurements."""
Kovrigin, Evgenii L; Kempf, James G; Grey, Michael J; Loria, J Patrick
Journal of magnetic resonance, 2006, Vol 180, p 93-104.
http://www.ncbi.nlm.nih.gov/pubmed/16458551
DOI: 10.1016/j.jmr.2006.01.010
Figure 9 and 10 shows these "rotten bananas".
Clustering data, in some way overcome this problem.
Since you now starts to add more data, compared to number of fitting
parameters.
The problem though, is that if you start from "single fitted" data,
and go to "Clustering of data", that
an average of the global parameter will be taken for the single fitted data.
In previous version of relax (a version or two ago), we changed from
taking the average to take the median of the parameters.
This was to prevent taking the average of an outliers, if one of the
single fitted spins have been fitted "crazy".
You don't want to start with a global kex at 10000.
I have discussed the CR72 Full model with my supervisor.
He have actually never seen it in use in any paper.
Always the assumption R20A=R20B is used.
If you only have one field, I would not even try this model.
If you still would like to try it, please consider using the B14 full
model as well, to compare.
http://wiki.nmr-relax.com/B14_full
Abstract: "Faithful estimation of dynamics parameters from CPMG
relaxation dispersion measurements."
This work examines the robustness of fitting of parameters describing
conformational exchange (k(ex), p(a/b), and Deltaomega) processes from
CPMG relaxation dispersion data. We have analyzed the equations
describing conformational exchange processes for the intrinsic
inter-dependence of their parameters that leads to the existence of
multiple equivalent solutions, which equally satisfy the experimental
data. We have used Monte-Carlo simulations and fitting to the
synthetic data sets as well as the direct 3-D mapping of the parameter
space of k(ex), p(a/b), and Deltaomega to quantitatively assess the
degree of the parameter inter-dependence. The demonstrated high
correlation between parameters can preclude accurate dynamics
parameter estimation from NMR spin-relaxation data obtained at a
single static magnetic field. The strong parameter inter-dependence
can readily be overcome through acquisition of spin-relaxation data at
more than one static magnetic field thereby allowing accurate
assessment of conformational exchange properties.
Troels Emtekær Linnet
PhD student
Copenhagen University
SBiNLab, 3-0-41
2014-09-09 9:48 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi Chung-ke,
Welcome to the relax mailing lists! Thanks to the hard work of one of
the relax developers - Troels Linnet - this long calculation time
should now be much, much shorter. Have a look at the following
release announcement:
http://wiki.nmr-relax.com/Relax_3.3.0
For the 'CR72 full' model (http://wiki.nmr-relax.com/CR72_full), the
clustering example here gives a ~22x speed up so your calculation time
would then drop from ~20,000 min to ~1000 min. If you would like to
receive announcements about new relax versions, please subscribe to
the relax-announce mailing list
(https://mail.gna.org/listinfo/relax-announce/). This list only
receives ~10 emails per year. See
http://news.gmane.org/gmane.science.nmr.relax.announce.
I have a few questions about how you performed the analysis. Did you
use a non-clustered set of results to seed the clustered analysis? In
the dispersion auto-analysis protocol exposed via the GUI, the results
from the non-clustered analysis will be taken as the starting point
for optimisation of the clustered analysis, as described in Morin et
al., 2014 (http://dx.doi.org/10.1093/bioinformatics/btu166). If you
wish, and are capable with scripting, you can also create your own
analysis protocol via a relax script and not use the auto-analysis.
The relax software is very flexible and you can create quite complex
analysis protocols - the auto-analyses are just large relax scripts.
Also, did you look at the results from the non-clustered analysis to
see if the kinetics of all 13 residues are similar? Or if the
dispersion curves look reasonable? Some data might be of low quality
and causing difficulties with the optimisation. You should also note
that most dispersion data is not good enough to differentiate R20A
from R20B. Do the final results (non-clustered and clustered) look
reasonable for these two parameters? It could be that differentiating
R20A from R20B in your system is difficult and causing optimisation to
take much longer than normal. Do you see the same optimisation times
with the clustered CR72 model where R20A=R20B=R20
(http://wiki.nmr-relax.com/CR72)? Also, have a look at the log file
from the analysis and see if the total number of minimisation
iterations is much longer for the 'CR72 full' model compared to the
CR72 model. This will tell you if the optimisation problem is much
more complicated for the 'full' model.
Regards,
Edward
On 9 September 2014 09:19, Chung-ke Chang <chungke@xxxxxxxxxxxxxxxxxx>
wrote:
Dear all,
This is my first post here, and I have a question regarding the time it
takes for a relaxation dispersion clustering process to finish. I have
one clustering calculation that has been running for ~ 20,000 min on a
single Xeon 2.66 GHz core. The cluster consists of 13 residues being fit
to the ‘CR72 full’ model. I wonder if the long time it is taking is
normal? Would it be possible that relax has been stuck in an infinite
loop of some sort, without showing up in the log file? Any input would be
greatly appreciated. By the way, using a cluster of only 11 residues out
of the 13 did finish in ~13,000 min.
Chung-ke Chang
Biomacromolecular NMR Lab
Institute of Biomedical Science
Academia Sinica, Taiwan
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Re: Relaxation dispersion clustering calculation time