[gmx-users] How to justify when the trajectory reached equilibrium
lvqingjiejie at 163.com
Sat Jul 11 04:19:07 CEST 2015
I see. Thanks.
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
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
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