[gmx-users] How to justify when the trajectory reached equilibrium
lvqingjiejie at 163.com
Thu Jul 9 16:30:04 CEST 2015
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?
At 2015-07-09 19:41:09, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>On 7/8/15 9:48 PM, Qing Lv wrote:
>> 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
>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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