[gmx-users] How Long to Equlibrate?

Steffen Wolf swolf at bph.rub.de
Thu Jul 26 14:37:57 CEST 2007

Hi Mark,
well, equilibration is a tricy thing: Most simple would be the answer
"when all observables level off", but one can wait eternally for that. I
usually go the folloing way:

a) has the total system energy levelled off / does it not fall anymore
but oscillates around a certain value?
b) are the interaction energies for the part of my system of interest
stable (for you: the protein/protein or protein/solvent terms) not
changin anymore / oscillating around a mean value?

An other painfull truth: don't expect anything like an equilibration
within 100 ps. After 2 ns most of the system creation effects (too high
order of solvent, lacking protein solvation etc.) will vanish, but then
comes the interesting part where the small but important changes happen.
In general: You NEVER can be sure that your system is equillibrated,
there might be changes even after 100 ns. A reasonable time scale for
simulations would be ca. 10 ns (if you can afford it computationally),
and see what you can gain as information out of this trajectory.

Hope this helps you - it's not really a cheerful positive answer, but
even in silico, nature is a bitch... ;)

> 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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Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de 

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