For reference, this message thread is irreversibly archived in multiple locations:
http://thread.gmane.org/gmane.science.nmr.relax.devel/4219, http://www.mail-archive.com/[email protected]/msg04137.html, http://marc.info/?t=137456469600001&r=1&w=2, https://mail.gna.org/public/relax-devel/2013-07/msg00097.html Regards, Edward On 23 July 2013 09:28, Edward d'Auvergne <[email protected]> wrote: > Hi, > > The 2-site numeric dispersion models for CPMG data are now fully > functional within relax! The following describes how these are implemented > in relax (to be permanently archived at > http://dir.gmane.org/gmane.science.nmr.relax.devel). I hope that you > will check all of this by running relax and seeing for yourself. I also > have a few questions below. Note that the code is in the relax_disp branch > of the source code repository and that there is no official release at > http://www.nmr-relax.com/download.html yet. > > I have documented the numeric models now present in relax in Chapter 10 of > the user manual. I have compiled the current manual for the branch and > uploaded it to http://download.gna.org/relax/manual/relax_disp_manual.pdf. > Please have a look and see what you think. The text is extremely minimal > and needs to be expanded. If you have any suggestions or additional > material (equations, figures, etc., and in LaTeX preferably), it would be > happily accepted. For example equations for the matrices and the > propagation used. The aim is to be a complete stand-alone relaxation > dispersion reference for the users, pointing them to all the relevant > literature at all possible points. Cheers! > > As a summary, from the relax_disp.select_model user function description, > the numeric models are: > > 'NS 2-site 3D': The reduced numerical solution for the 2-site > Bloch-McConnell equations using 3D magnetisation vectors whereby the > simplification R20A = R20B is assumed. Its parameters are {R20, ..., pA, > dw, kex}. > > 'NS 2-site 3D full': The full numerical solution for the 2-site > Bloch-McConnell equations using 3D magnetisation vectors. Its parameters > are {R20A, R20B, ..., pA, dw, kex}. > > 'NS 2-site star': The reduced numerical solution for the 2-site > Bloch-McConnell equations using complex conjugate matrices whereby the > simplification R20A = R20B is assumed. It has the parameters {R20, ..., > pA, dw, kex}. > > 'NS 2-site star full': The full numerical solution for the 2-site > Bloch-McConnell equations using complex conjugate matrices with parameters > {R20A, R20B, ..., pA, dw, kex}. > > 'NS 2-site expanded': The numerical solution for the 2-site > Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It > has the parameters {R20, ..., pA, dw, kex}. > > I would be interested to hear if you have suggestions for saner model > names. > > In the auto-analysis in relax - the blackbox analysis script to make the > lives of users extremely easy - the *full models are not turned on by > default. If curious, you can see auto-analysis script in the file > auto_analyses/relax_disp.py. The auto-analysis script is normally hidden > from the user. Also, please run the relax GUI with: > > $ relax --gui > > and start the relaxation dispersion analysis to see how it is > implemented. Note that the auto-analyses are used for the operation of all > GUI analyses. Using scripts, the relax user is free to do anything they > wish and implement any protocol they can imagine (if useful for other > users, these can then be converted into an auto-analysis). > > Part of the auto-analysis that I have implemented is the concept of using > optimised parameters from a simpler or equivalent model to speed up > optimisation by avoiding an expensive grid search. For the 'full' models > above, I use the parameters of the simpler model and start with R20A = R20B > = R20. Then, during optimisation, R20A and R20B diverge. > > For the model equivalence, this is a bit different. I use the optimised > parameter values from the analytic Carver and Richards model (CR72) as the > starting parameters for the 'NS 2-site 3D', 'NS 2-site star' and 'NS 2-site > expanded' models. This avoids the grid search and really speeds up the > optimisation by orders of magnitude. It can be done because the CR72 > results are often very similar to the numeric results. And even a failed > CR72 solution is close enough to the minima to be used as a starting point > for the numeric models. > > I have a few other implementation questions, but I'll send these in a > different message for saner threads in the mailing list archives. > > Cheers, > > Edward > > > P. S. Actually, I might take some of this text into the relax manual :) >
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