[gmx-users] How Long to Equlibrate?

Ran Friedman r.friedman at bioc.unizh.ch
Thu Jul 26 14:30:56 CEST 2007

Dear Mark,

Unfortunately there's no clear cut answer, and it depends on your
protein, the ensemble and what you'd like to measure. I'd certainly
examine the equilibration of thermodynamic parameters such as pressure,
temperature and energy components and verify that they equilibrate. You
can check the CA or backbone RMSD plot as well, both for values and for
changes. Also, check the literature for the equilibration times other
people have used, which should give you some indication.


Mark Zottola wrote:
> I have a 290+ residue protein and I recently ran a 200 ps simulation
> in a water box with electrostatic cutoff at approximately half the
> value of the box dimension.  Since there is no heating stage in the
> dynamics, I am wondering what guidelines there are for knowing when to
> evaluate data from the simulation.  There are some interesting
> features to the RMSD plot I would like to investigate. But I am not
> sure I can analyze the last 100 ps of the dynamics or not.  Any help
> would be greatly appreciated.
> Thanks!
> Mark

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