[AMBER] Accelerated Molecular Dynamics and convergence

From: Rosellen, Martin <martin.rosellen.16.ucl.ac.uk>
Date: Wed, 8 Jul 2020 13:58:20 +0000

Hi Amber mailing list,

I am comparing AMD simulations of two structures that are mainly differing in the twist angle of a hairpin. It was shown that with AMD both structures sample the same twist angle after around 500 ns. Is it legit to disregard the first 500 ns of both structures in a sense that this time is needed for both structures to converge? I am wondering because I consider convergence as reaching a thermodynamic equilibrium which is not the goal of AMD.

looking forward to your answers,

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Received on Wed Jul 08 2020 - 07:00:04 PDT
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