Hi Edward. I will change it to 20 for grid search.
I will modify the manual within a timeframe of a week. Best Troels 2014-09-27 13:04 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > If that's the case, then maybe grid searching from 0 to 20 would be > better? If it's higher than 20, the subsequent optimisation should > send it to the correct value. Also, what about adding this commit > message description of the limitations of the k_AB parameter to the > TSMFK01 section of the manual at > http://www.nmr-relax.com/manual/TSMFK01_2_site_CPMG_model.html? Oh, > all changes in the grid search values also needs to be updated in the > list at > http://www.nmr-relax.com/manual/Dispersion_parameter_grid_search.html. > > Cheers, > > Edward > > > > On 27 September 2014 12:20, <[email protected]> wrote: > > Author: tlinnet > > Date: Sat Sep 27 12:20:33 2014 > > New Revision: 26085 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=26085&view=rev > > Log: > > For relaxation dispersion, modified that the Grid search and linear > constraints for parameter "k_AB" is between 0-100. > > > > The parameter is only used in the TSMFK01 model. > > > > The "k_AB" parameter is only for very slow forward exchange rate. > > The extected values should according to the reference paper: > > > > Tollinger, M., Skrynnikov, N. R., Mulder, F. A. A., Forman-Kay, J. D., > and Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an > sh3 domain. J. Am. Chem. Soc., 123(46), 11341-11352. (10.1021/ja011300z) > > > > The paper conserns values of k_AB in the region 0.1 to 5.0. > > > > If the exchange rate is any higher value of this, then another model > should be used for the analysis. > > > > Modified: > > trunk/specific_analyses/relax_disp/parameter_object.py > > trunk/specific_analyses/relax_disp/parameters.py > > > > Modified: trunk/specific_analyses/relax_disp/parameter_object.py > > URL: > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameter_object.py?rev=26085&r1=26084&r2=26085&view=diff > > > ============================================================================== > > --- trunk/specific_analyses/relax_disp/parameter_object.py > (original) > > +++ trunk/specific_analyses/relax_disp/parameter_object.py Sat Sep > 27 12:20:33 2014 > > @@ -568,13 +568,13 @@ > > self._add( > > 'k_AB', > > scope = 'spin', > > - default = 1000.0, > > + default = 2.0, > > desc = 'The exchange rate from state A to state B', > > py_type = float, > > set = 'params', > > - scaling = 10000, > > - grid_lower = 1.0, > > - grid_upper = 10000.0, > > + scaling = 100, > > + grid_lower = 0.1, > > + grid_upper = 100.0, > > grace_string = '\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)', > > err = True, > > sim = True > > > > Modified: trunk/specific_analyses/relax_disp/parameters.py > > URL: > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameters.py?rev=26085&r1=26084&r2=26085&view=diff > > > ============================================================================== > > --- trunk/specific_analyses/relax_disp/parameters.py (original) > > +++ trunk/specific_analyses/relax_disp/parameters.py Sat Sep 27 > 12:20:33 2014 > > @@ -446,11 +446,10 @@ > > padw2 >= 0 > > dw >= 0 > > 0 <= kex <= 2e6 > > - 0 <= k_AB <= 2e6 > > 0 <= kB <= 2e6 > > 0 <= kC <= 2e6 > > + 0 <= k_AB <= 100 > > tex >= 0 > > - k_AB >= 0 > > > > > > Matrix notation > > @@ -504,9 +503,11 @@ > > | | | | | | > > |-1 0 0 | | kC | | -2e6 | > > | | | | | | > > + | 1 0 0 | | k_AB | | 0 | > > + | | | | | | > > + |-1 0 0 | | k_AB | | 100 | > > + | | | | | | > > | 1 0 0 | | tex | | 0 | > > - | | | | | | > > - | 1 0 0 | | k_AB | | 0 | > > > > > > @keyword spins: The list of spin data containers for > the block. > > @@ -621,13 +622,23 @@ > > break > > > > # Exchange rates and times (0 <= k <= 2e6). > > - elif param_name in ['kex', 'kex_AB', 'kex_AC', 'kex_BC', > 'k_AB', 'kB', 'kC']: > > + elif param_name in ['kex', 'kex_AB', 'kex_AC', 'kex_BC', 'kB', > 'kC']: > > A.append(zero_array * 0.0) > > A.append(zero_array * 0.0) > > A[j][param_index] = 1.0 > > A[j+1][param_index] = -1.0 > > b.append(0.0) > > b.append(-2e6 / scaling_matrix[param_index, param_index]) > > + j += 2 > > + > > + # Exchange rates and times (0 <= k_AB <= 100). > > + elif param_name in ['k_AB']: > > + A.append(zero_array * 0.0) > > + A.append(zero_array * 0.0) > > + A[j][param_index] = 1.0 > > + A[j+1][param_index] = -1.0 > > + b.append(0.0) > > + b.append(-100. / scaling_matrix[param_index, param_index]) > > j += 2 > > > > # Exchange times (tex >= 0). > > > > > > _______________________________________________ > > relax (http://www.nmr-relax.com) > > > > This is the relax-commits 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-commits > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel 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-devel > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel 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-devel
