[gmx-users] Equilibrium state

[Justin Lemkul]

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.
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