[gmx-users] How to justify when the trajectory reached equilibrium

[Justin Lemkul]

On 7/8/15 9:48 PM, Qing Lv wrote:
> Hi,
>
> 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 
converged.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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