[MMTK] Energy minimization

Новиков Глеб 0wn3r at bk.ru
Tue Oct 11 18:34:58 UTC 2011


Greetings!

I wounder to know about algoritms of energy minimization presented in the MMTK. What exactly type of that algoritms is most suitable for the common proteins ( 2000-5000 atoms ) ?  I've tried to use the example script for energy minimization
minimizer = ConjugateGradientMinimizer(universe,
 actions=[StandardLogOutput(50)])
minimizer(convergence = 1.e-3, steps = 10000)


but this is very slow for my proteins ( I've tested different proteins like typical globular lyzocyme).

What average number of steps I should define for my proteins for obtaining well minimized universe ? Also I wounder to know about minimization of membrane proteins? Does this
procedure must be conducted in the explicit membrane environment or the simulation in the vacuum would be reasonable?

Finally small qustion about scripting :) If I save my universe in pdb after minimization e.g


universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('bala1')


minimizer = ConjugateGradientMinimizer(universe,
 actions=[StandardLogOutput(50)])
minimizer(convergence = 1.e-3, steps = 10000)

universe.writeToFile('insulin_with_h.pdb')

does I obtain minimized structure of my protein?

Thank you for your help,

Gleb






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