Hi Ed, - technically, yes: phenix.refine model.pdb data.mtz strategy=individual_sites target_weights.wxc_scale=0 main.bulk_sol=false simulated_annealing=true simulated_annealing.mode=every_macro_cycle In addition, you may want to change the temperature, number of macro-cycles, etc.... - 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. Pavel. 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?
Ed.