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

[Justin Lemkul]

On 7/9/15 10:11 AM, Qing Lv wrote:
> Thank you, Justin.
> I am trying to simulate a protein-ligand complex to see the conformation transition during the simulation... We propose that the receptor pocket may be subject to a conformational change upon ligand-binding, so I want to verify it by MD...
> I am really a newbie in molecular simulation and all I did to analysis were time evolution of RMSD, interaction energy, and visualization. I try to do some principal component analysis, but literature said that PCA must be performed after equilibrium...
>

If you are hypothesizing a conformational change, then you need a way to 
quantify that change - distances, angles, etc.

> Could you give me more info on block-averaging, or any other advice that will help?
>

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.

-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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