[phenixbb] refinement - p.s.

[Pavel Afonine]

Forgot to mention: for the Cartesian dynamics the command would be : 
simulated_annealing=true

Pavel.


On 12/8/09 6:06 PM, Pavel Afonine wrote:
> Hi Pei-Chun,
>
>   
>> What command should I use to do Cartesian or torsion-angle simulated
>> annealing?
>>     
>
> simulated_annealing_torsion=true
>
> For example:
>
> phenix.refine model.pdb data.mtz your_parameters.params
> simulated_annealing_torsion=true
>
> If you run it from the GUI, then I guess there will be an obvious
> check-box for this.
>
> Pavel.
>
>   
>> Where should I change if I want to run .eff?
>> }
>> simulated_annealing {
>> start_temperature = 5000
>> final_temperature = 300
>> cool_rate = 100
>> number_of_steps = 25
>> time_step = 0.0005
>> n_print = 100
>> update_grads_shift = 0.3
>> refine_sites = True
>> refine_adp = False
>> max_number_of_iterations = 25
>> mode = every_macro_cycle *second_and_before_last once first
>> verbose = -1
>>     
>
> The default seatings above look good to me. You may try "aggressive" SA
> by increasing the start_temperature, say up to 10000K or so. Of course,
> you need to have a clear idea why to do so in your particular case.
>
> Pavel.
>   
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