[phenixbb] Output for den optimization runs

Jeff Headd jjheadd at lbl.gov
Mon Jan 9 16:11:08 PST 2012


My only other suggestion would be to try and use Cartesian simulated
annealing instead. Sometimes I've found that this method performs
better.

Jeff

On Mon, Jan 9, 2012 at 3:44 PM, Francis E Reyes
<Francis.Reyes at colorado.edu> wrote:
> Any other recommendations for the simulated annealing run besides lowering the starting temperature when you have a model that's mostly (90%) placed?
>
>
>
> Thanks!
>
> F
>
> On Jan 9, 2012, at 3:37 PM, Jeff Headd wrote:
>
>> Hi Francis,
>>
>> At the moment the only way to change the starting temperature is to do
>> so in the 'tardy' scope. This would look like:
>>
>> refinement {
>>  tardy {
>>    start_temperature_kelvin = 2500
>>    final_temperature_kelvin = 300
>>  }
>>
>> Adding DEN-specific control is on my to-do-list.
>>
>> Jeff
>>
>> On Mon, Jan 9, 2012 at 2:23 PM, Francis E Reyes
>> <Francis.Reyes at colorado.edu> wrote:
>>> Is there an option to specify the starting torsion simulated annealing temperature when den.optimize=True ?
>>>
>>> F
>>>
>>> On Jan 9, 2012, at 10:45 AM, Jeff Headd wrote:
>>>
>>>> Hi Francis,
>>>>
>>>> Each DEN optimization step outputs a lot of information, so at present
>>>> the code suppresses that information and only a summary will be
>>>> printed at the conclusion of optimization.
>>>>
>>>> I can add an option for verbose output, though if the job is running
>>>> on multiple cores the logs would need to be written after all jobs
>>>> have completed for the output to be readable.
>>>>
>>>> Jeff
>>>>
>>>> On Mon, Jan 9, 2012 at 9:39 AM, Francis E Reyes
>>>> <Francis.Reyes at colorado.edu> wrote:
>>>>> Is there a refine.log for each den (gamma, weight) optimization? I can't seem to find one anywhere and I'm curious to see how it's doing.
>>>>>
>>>>> Thanks!
>>>>>
>>>>> F
>>>>>
>>>>> ---------------------------------------------
>>>>> Francis E. Reyes M.Sc.
>>>>> 215 UCB
>>>>> University of Colorado at Boulder
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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