[phenixbb] Set up Simulated Annealing starting tempreture

[Xiao Lei]

Hi Pavel,

Thank you very much for the information. It works in my Phenix!

Xiao



On Mon, Jul 13, 2015 at 5:09 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hello Xiao,
>
> if you use the command line to run programs then the line you quoted
> illustrates how to change the temperature.
>
> If you are using the GUI, for Cartesian SA:
>
> Refinement settings -> All parameters -> Advanced -> Simulated annealing
>
> for torsion SA:
>
> Refinement settings -> All parameters -> Advanced -> Torsion angle dynamics
>
> This will pop up a window where you can change the default temperature.
>
> Pavel
>
>
>
> On 7/13/15 16:50, Xiao Lei wrote:
>
>> Dear Phenixbb members,
>>
>> I'm learning phenix this days. I use phenix refinement and found there is
>> a simulated annealing option (SA Cartesian or SA torsion option). However,
>> I found the SA cartesian starts at 5000K and SA torsion starts at 2500K by
>> default, and I'd like to change the starting temperature by myself.  I
>> search phenix manual and found:
>>
>> To change starting SA temperature:
>>
>> % phenix.refine data.hkl model.pdb simulated_annealing=true \
>>   strategy=individual_sites simulated_annealing.start_temperature=10000
>>
>>
>> I do not understand this, does this mean I have to type the above command
>> in somewhere in phenix? is there a place I can simply put SA start
>> temperature numbers in?
>>
>> Xiao
>>
>>
>
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