Re: r26085 - in /trunk/specific_analyses/relax_disp: parameter_object.py parameters.py -- September 27, 2014 - 13:04

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,  <tlinnet@xxxxxxxxxxxxx> 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).
>
>
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