Rick Venable wrote:
 For a solvated protein simulation, I'd monitor the potential energy, the
 radius of gyration, and the bacbone RMSD relative to the starting
 structure.  When all 3 of these become flat, one could argue that
 the system is equilibrated; this could require 100s of picoseconds.
 Although indeed one can argue this, it is hard to tell what 'flat' means
 in a practical sense. For a seond-year lecture I give I have three slides
 each giving the rmsd of a protein w/r to the x-ray structure. All three
 of them level off to a nice plateau at the end, and appear to be genuinly
 equilibrated in the way you define that. But, the three plots are of the
 same simulation, the first of 0-100ps, the second of 0-1ns, and the last
 of 0-10ns! If you overlay them, they are almost the same, except for the
 scale of the axes! Those of you who'd like to see them, please ask me and
 I can send you the three jpg files (~50k each).
 While I don't regularly monitor r_gyr or e_pot, I don't know but suspect
 that they would show similar behaviour... (although they may equilibrate
 much faster than the rmsd).
  _____________ _______________________________________________________
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 |  _   _  ___,| K. Anton Feenstra                                     |
 | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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