[AMBER] Equilibirum/System convergence

From: Parker de Waal <Parker.deWaal.vai.org>
Date: Thu, 31 Jul 2014 17:15:37 +0000

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.


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Received on Thu Jul 31 2014 - 10:30:03 PDT
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