[phenixbb] Output for den optimization runs

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Jan 9 15:44:52 PST 2012


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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