I used the expression like this:
grid_search(lower=[0.111, 0, 0], upper=[0.111, 2, 1E12], inc=[1, 11, 11])
But I get the following error:
Unconstrained grid search size: 121 (constraints may decrease this size).
Traceback (most recent call last):
File "/usr/local/bin/relax", line 418, in <module>
Relax()
File "/usr/local/bin/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/usr/local/relax/prompt/interpreter.py", line 276, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 537, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 433, in
interact_script
execfile(script_file, local)
File "mf_multimodel_m5S2f0111.py", line 82, in <module>
grid_search(lower=[0.111, 0, 0], upper=[0.111, 1, 11], inc=[1, 11, 11])
File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 479,
in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 922,
in minimise
min_options = self.grid_search_config(num_params, spin=spin,
lower=lower, upper=upper, inc=inc, scaling_matrix=scaling_matrix)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 554,
in grid_search_config
self.grid_search_config_fin(min_options, lower, upper, scaling_matrix)
File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 631,
in grid_search_config_fin
for i in xrange(n):
NameError: global name 'n' is not defined
Any ideas?
Cheers
Tiago
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Edward d'Auvergne
Sent: quarta-feira, 6 de Abril de 2011 18:05
To: Tiago Pais
Cc: [email protected]
Subject: Re: How to set S2f to 0.111?
Hi,
These match the parameters as listed in the help for the
model_free.select_model() user function. The grid search arrays match
the parameter arrays.
Regards,
Edward
On 6 April 2011 18:54, Tiago Pais <[email protected]> wrote:
> Ok,
> Im sorry to insist but I am probably missing something here. How do I
state
> which bound goes with which parameter? That is, which position in the
array
> bound corresponds to the S2f parameter?
> Regards.
> TP
>
> -----Original Message-----
> From: [email protected] [mailto:[email protected]] On
> Behalf Of Edward d'Auvergne
> Sent: quarta-feira, 6 de Abril de 2011 17:42
> To: Tiago Pais
> Cc: [email protected]
> Subject: Re: How to set S2f to 0.111?
>
> Hi,
>
> That is roughly correct. Just set the lower and upper bound to 0.111
> and set the number of increments for that parameter to 1. Then it is
> like a grid search without S2f being present, or being fixed to 0.111.
>
> Regards,
>
> Edward
>
>
>
> On 6 April 2011 18:38, Tiago Pais <[email protected]> wrote:
>> Hi Ed,
>> Thanks for the quick reply.
>> Let's see if I understand your suggestion. For example, the
> mf_multimodel.py
>> sample script performs a grid search minimization using the grid_search
>> function. So if I insert an array of upper and lower bounds for the
>> parameters in the model I can constrain the interval of possible results,
>> correct? If so, what is the sequence for the parameters in the array?
>> TP
>>
>>
>>
>> -----Original Message-----
>> From: Edward d'Auvergne [mailto:[email protected]]
>> Sent: quarta-feira, 6 de Abril de 2011 17:13
>> To: Tiago Pais
>> Cc: [email protected]
>> Subject: Re: How to set S2f to 0.111?
>>
>> Hi,
>>
>> Unfortunately, there is no ability to fix one of the model-free
>> parameters during optimisation in relax yet. This is something that
>> has been requested one or two times over the years. This is
>> complicated as the gradients and Hessians (first and second partial
>> derivates) need to be modified with this in mind, as the curvature of
>> the space changes. The fixed parameter is not part of the gradient or
>> Hessian, and has to be removed. This really complicates the target
>> function, gradient, and Hessian and, due to the low demand, has not
>> been implemented.
>>
>> Are you able to optimise this parameter and see if you get 0.111? And
>> are you able to extract the timescale of this process (the methyl
>> group rotamer jumps)? From memory, someone has optimsed these models
>> using a grid search. This coarse optimisation can be performed in
>> relax as you are able to specify the fine details of the grid search.
>> It is slower, but will do the job. You could even implement a zooming
>> grid search if your scripting skills are up to it to be able to
>> relatively quickly find the parameters to high precision. Anyway, I
>> hope this info helps.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>>
>>
>> On 6 April 2011 17:39, Tiago Pais <[email protected]> wrote:
>>> Hi,
>>>
>>> I would like to make an analysis of side-chain relaxation data with the
>> S2f
>>> parameter (in model 5) set to 0.111.
>>>
>>> Is it possible to do this with RELAX? How?
>>>
>>> Thanks in advance.
>>>
>>> Cheers
>>>
>>> Tiago P
>>>
>>>
>>>
>>> **************************************
>>>
>>> Tiago Pais, PhD. student
>>>
>>> Cell Physiology & NMR
>>>
>>> Instituto de Tecnologia Química e Biológica-Oeiras
>>>
>>>
>>>
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