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

[Qing Lv]

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...

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

Best,
Qing


At 2015-07-09 19:41:09, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 7/8/15 9:48 PM, Qing Lv wrote:
>> Hi,
>>
>> I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium...
>> Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any methods/criteria to justify the equilibrium other than RMSD evolution?
>>
>
>RMSD is pretty useless in telling you anything about convergence.  Great, your 
>structure probably isn't changing a whole lot (but RMSD can also hide 
>interesting things).  Assess convergence based on the quantities of interest - 
>why did you do the simulation?  What behavior are you trying to observe, and 
>what measurables do you use to assess it?  If those metrics are invariant with 
>time (e.g. via block-averaging or something) then your simulation is likely 
>converged.
>
>-Justin
>
>-- 
>==================================================
>
>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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