This should save a lot of computation time, not spending so much effort searching in an invalid region of the parameter space.
Cheers! Edward On 27 September 2014 16:33, Troels Emtekær Linnet <[email protected]> wrote: > 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
