Hi Edward, > Did you run relax with Gary Thompson's multi-processor > framework to take advantage of all your CPU cores?
Yes, I used mpi4py. And in fact it's a hexacore Intel Core i7, not an octocore. I'm not sure if I should run mpi4py with the six physical number of cores or with the double of that numbers (12 hyperthreaded cores). >> Now I tried a big protein–one with >240 assigned residues. It took 2 days >> and 23 rounds to find a optimized spherical diffusion model, and since >> yesterday it churned out 35 prolate diffusion models! > > This is quite possible. I would highly recommend you create plots of > the progression of optimisation such as in: [d'A&G:2008b] > > You can obtain the data for the plots by manually opening the results > files in the 'opt' directories and then manually creating the graphs. I stopped the process after relax made >100 prolate models and tried to extract the mentioned parameters (tm, total number of parameters k, global AIC, chi2) from the results files in round_x/opt/ to see where it is heading. Turns out this appears to be more difficult than expected. I can see the chi2 values and all the model-free parameters like S^2 and R_ex, but how can I get the AIC or the total number of parameters from? Is there a relax function which lists all the parameters of the current data pipe? > [...] It could be that you are in almost perpetual motion orbiting around two > solutions, sliding in and > out of different optimisation spaces or universes, one day colliding with one > of them (see below). > If the complex exhibits domain motions, then this could explain the > long optimisation times (though not definitively). Actually I don't expect anything like that. > I hope this description is not too abstract. Your explanations are – as always – very verbose and comprehensible in the most positive way! Cheers Martin -- Martin Ballaschk AG Schmieder Leibniz-Institut für Molekulare Pharmakologie Robert-Rössle-Str. 10 13125 Berlin [email protected] Tel.: +49-30-94793-234/315 Büro: A 1.26 Labor: C 1.10 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
