[phenixbb] MD with phenix.refine?
pafonine at lbl.gov
Fri Aug 20 16:03:35 PDT 2010
- technically, yes:
phenix.refine model.pdb data.mtz strategy=individual_sites
target_weights.wxc_scale=0 main.bulk_sol=false simulated_annealing=true
In addition, you may want to change the temperature, number of
- practically, no, this will all probably not make much sense since the
restraints target does not have an attractive term (does not account for
electrostatics). So your MD run will likely unfold your protein. To some
extent you may correct for this by using secondary-structure restraints
or your manually defined restraints, but still it's not the same...
MD in phenix.refine is just a tool for optimization and was never meant
to be a proper MD tool.
On 8/20/10 3:53 PM, Ed Pozharski wrote:
> Silly question:
> is there some way to run what would essentially be an MD simulation with
> phenix.refine? I mean, turn off X-ray-term by setting
> tardy.target_weights.fix_wxc=0, and then run cartesian dynamics?
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