[gmx-users] Equilibrium state

[Александр Лашков]

Also in some case (for example TI) you may use auto correlation time to
detect equilibrium region.See: A Simple Method for Automated Equilibration
Detection in Molecular Simulations. Chodera JD. J Chem Theory Comput. 2016.


Alexander Lashkov

сб, 21 дек. 2019 г., 17:25 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 12/21/19 3:22 PM, Justin Lemkul wrote:
> >
> >
> > On 12/21/19 12:49 PM, elham wrote:
> >> Dear all,
> >> How can we find out the equilibrium state is reached after 20ns NVT
> >> simulation?
> >> Do the potential energy plot confirm the equilibrium state? or other
> >> analysis is required to prove the equilibrium state?
> >
> > Potential energy does not tell you this, but you can demonstrate that
> > the proper thermodynamic ensemble has been reached by analyzing the
> > temperature/kinetic energy and associated distribution to ensure that
> > it matches a canonical ensemble.
> >
>
> I should also add - the above refers to equilibrium of the statistical
> mechanical ensemble, but if you want to establish
> convergence/equilibrium of sampling, then you have to analyze all
> relevant structural, dynamical, and thermodynamical properties of
> interest within your system. For example, 20 ns is certainly more than
> enough to reach equilibrium with respect to temperature (by orders of
> magnitude) but is probably about 100x too short to establish equilibrium
> sampling of an intrinsically disordered protein.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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