I've always liked this classic (but somewhat old now) article
Assessing Equilibration and Convergence in Biomolecular Simulations
Lorna J. Smith, Xavier Daura, and Wilfred F. van Gunsteren
http://bioinf.uab.cat/xavier/papers/proteins_48-487.pdf
On Tue, Mar 2, 2021 at 8:31 PM B. Lachele Foley <lfoley.ccrc.uga.edu> wrote:
> I have no strong opinions on this, but others, notably Adrian, do. I want
> to make sure I have the same understanding of these words as others.
>
> The following definitions are what I think others mean and are intended as
> a starting point for better definitions. Do you agree with them? If not,
> what should they be? Or what words would you give for these definitions?
> I tried to avoid deep stat-mech/thermo terminology.
>
> Relaxed (commonly called 'equilibrated'):
> In practical terms, the system has entered a stationary phase with respect
> to bulk properties that are expected to be in stationary phase per the
> simulation setup but that are not being held constant. These will
> typically include one or more of total energy, pressure, volume, density,
> and temperature. With respect to physics, this means that the simulated
> system has probably begun to sample configurations of mass and energy
> (momentum) in proportions consistent with the simulated ensemble (not
> necessarily the reality being modeled).
>
> Converged:
> For some property, not necessarily a bulk property, a stationary phase,
> which might unimodal or multimodal, has been sampled enough that meaningful
> statistical descriptions might be made about it. The system has sampled
> very well, in ensemble-appropriate proportions, a persistent or metastable
> subset of the phase space.
>
> Equilibrated:
> The entire system has sampled all available configurations sufficiently
> that meaningful statistics can be made about any system property. That is,
> the system has thoroughly sampled an ensemble-appropriate portion of the
> phase space, in ensemble-appropriate proportions, multiple times.
>
> Most simulations of any significant complexity can only hope to attain
> 'converged' with respect to whatever properties are being tracked. It is
> very difficult to know for certain that other behaviors would not be
> observed were the simulation to be run longer. I think if there were an
> easy way to tell, then we would not very often need to do simulations.
> This problem also impacts our ability to know if 'relaxed' is truly
> 'relaxed', etc.
>
> :-) Lachele
>
> Dr. B. Lachele Foley (she/her/hers)
> Associate Research Scientist
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> http://glycam.org
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Received on Wed Mar 03 2021 - 07:30:02 PST
