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Forgot to mention: for the Cartesian dynamics the command would be :
simulated_annealing=true<br>
<br>
Pavel.<br>
<br>
<br>
On 12/8/09 6:06 PM, Pavel Afonine wrote:
<blockquote cite="mid:4B1F0625.9010903@lbl.gov" type="cite">
<pre wrap="">Hi Pei-Chun,
</pre>
<blockquote type="cite">
<pre wrap="">What command should I use to do Cartesian or torsion-angle simulated
annealing?
</pre>
</blockquote>
<pre wrap=""><!---->
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.
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap=""><!---->
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.
</pre>
</blockquote>
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