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

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 <edward@xxxxxxxxxxxxx>:

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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Re: r26085 - in /trunk/specific_analyses/relax_disp: parameter_object.py parameters.py

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