Re: [AMBER] Equilibirum/System convergence

From: Carlos Simmerling <>
Date: Thu, 31 Jul 2014 13:33:38 -0400

Hi Parker,
in your case I might agree with the reviewers in wanting to know what you
mean. If you said that there was an equilibrium between closed and open,
and the (thermodynamic) partitioning between the 2 states was not changing
with longer runs, then it's clear that you mean a thermodynamic equilibrium
for these 2 substates. If it just closes, I'm not sure either what you mean
by equilibrium. One could as well say that the loop "became kinetically
trapped" in the closed substate. Maybe they want you to define what you
think equilibrium means for your conclusions, rather than just how you
measured it. One you have an idea of what you mean, it's easier to say how
you're sure that's the case.

On Thu, Jul 31, 2014 at 1:15 PM, Parker de Waal <>

> Hello Everyone,
> This morning I received feedback on a recently submitted manuscript and
> one of the reviewers asked us how to explicitly define how we determined
> our system had converged, or reached the equilibrium state during our long
> scale production run. Before our initial submission I had done a literature
> search for criteria to determine if the system had reached an EQ state,
> however it seems as though this is a grey area and varies greatly between
> groups/literature/forums depending on who you ask.
> For my case, the protein has a gating loop that reached an EQ state in the
> closed confirmation when bound to a ligand however both reviews asked for
> an explanation as to how we determined this is in EQ (besides backbone
> RMSD). If anyone could off any advice I would greatly appreciate it.
> Best,
> Parker
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Received on Thu Jul 31 2014 - 11:00:02 PDT
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