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

[Justin Lemkul]

On 7/9/15 11:00 PM, Qing Lv wrote:
>> It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether or not the quantities of interest are varying over time or if they are stable, i.e. converged.
>
>
> Thank you, Justin.
> What size of blocks I need to divide in such an analysis? e.g., for a 100-ns trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if it has converged?
>

There are no hard and fast rules here.  It all depends on the frequency of your 
sampling and the time scale of the behavior(s) of interest.  Only you can figure 
those things out based on the goals of your work and your protocols for 
collecting data.

-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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