Just to clarify my point of view.
I agree 100% with Lachele's categories, very well done !
What I 'object' to is that we spend lots of time telling students about
equilibrium, about Boltzmann distributions, about high barriers and
sampling, meaning that true equilibrium is close to impossible, and THEN
we say 'the MD is equilibrated', which literally means 'it has reached
equilibrium'.
That is all, just the confusing statements, which are not needed. In
Monte Carlo people use 'burn time' to say 'we will throw away the first
10% of the trajectory for example. They would never call say 'the first
10% is equilibration'.
Adrian
On 3/3/21 10:12 AM, Carlos Simmerling wrote:
> [External Email]
>
> 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
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinf.uab.cat_xavier_papers_proteins-5F48-2D487.pdf&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=_3pixpATB1Be1J-EMpIY0KxbinKlXLcKVfe2WinaGaQ&s=JTEdzpPljAaho1e2S2mS2_QUyCNF1oPXgJSEIpJPtSo&e=
>
> 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
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__glycam.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=_3pixpATB1Be1J-EMpIY0KxbinKlXLcKVfe2WinaGaQ&s=4OkXbmqV-qKszwk_QR1MTKSt7cGhHyruhlNNzM4CRRk&e=
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Mar 03 2021 - 08:00:02 PST
