Minimizing and Equilibrating

From: a-yermakova_at_northwestern.edu
Date: Mon Jul 17 2006 - 13:12:52 CDT

('binary' encoding is not supported, stored as-is) I am working with a protein solvated in a water box (altogether 450,000atoms). As the tutorial
suggests, I am going to

1)minimize the system
2)fix the proteins and equilibrate
3) minimize and equilibrate again, with protein free to move.

I am looking for suggestions regarding the number of timesteps needed for each one of those steps.
Should there be more equilibration TS's than minimization? If so, are there any suggested relative
proportions? Should the first and second minimizations/equilibrations have the same number of
timesteps? How significant is this?

Thank you very much!
Anya Yermakova

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