[gmx-users] How to justify when the trajectory reached equilibrium
jalemkul at vt.edu
Fri Jul 10 23:07:40 CEST 2015
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
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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