[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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