Re: [AMBER] Sufficiently equilibrated or not

From: Delwakkada Liyanage, Senal Dinuka <sdd313.msstate.edu>
Date: Sat, 20 Feb 2021 19:46:01 +0000

Hello Dr. Foley,

Thank you for your feedback. If I may ask, is that due to the rising nature of rmsd or rapid fluctuations of the points?

Senal Liyanage
________________________________
From: Lachele Foley <lf.list.gmail.com>
Sent: Saturday, February 20, 2021 1:41 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Sufficiently equilibrated or not

I would not consider the system in that image to be equilibrated.

On Sat, Feb 20, 2021 at 2:17 PM Delwakkada Liyanage, Senal Dinuka
<sdd313.msstate.edu> wrote:
>
> Dear Amber Users and Developers,
>
> Here I have attached is a rmsd plot obtained for a ~100 ns equilibrated trajectory (saved at every 10 ps) of a DNA/ligand system. I am attempting to calculate absolute binding free energy through a thermodynamic integration (TI) approach. I was hoping if you could clarify to me whether the system is equilibrated enough to proceed with the TI calculations. I was under doubt due to the fluctuations shown throughout the last 6000 frames (60 ns). I understand there isn't an exact answer to this. But I appreciate your opinion on this.
> [cid:f8200194-9003-4107-accf-086dd0f15353]
>
> Thank you
>
> Senal Liyanage
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Feb 20 2021 - 12:00:03 PST
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