[gmx-users] How to justify when the trajectory reached equilibrium
jalemkul at vt.edu
Thu Jul 9 13:41:22 CEST 2015
On 7/8/15 9:48 PM, Qing Lv wrote:
> I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium...
> Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any methods/criteria to justify the equilibrium other than RMSD evolution?
RMSD is pretty useless in telling you anything about convergence. Great, your
structure probably isn't changing a whole lot (but RMSD can also hide
interesting things). Assess convergence based on the quantities of interest -
why did you do the simulation? What behavior are you trying to observe, and
what measurables do you use to assess it? If those metrics are invariant with
time (e.g. via block-averaging or something) then your simulation is likely
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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