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

[Qing Lv]

I see. Thanks.

Qing



At 2015-07-11 05:07:27, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>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
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
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>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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