Hello Dr. Foley,
Thank you very much for your valuable input.
Senal Liyange
________________________________
From: Lachele Foley <lf.list.gmail.com>
Sent: Saturday, February 20, 2021 1:55 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Sufficiently equilibrated or not
It's due to the rising nature, mostly. But, you also need stable
fluctuations. That is, if you have a significant change in the
amplitude of the fluctuation or if there is a trend (rising or
falling) in the data, then the system is not equlibrated.
On Sat, Feb 20, 2021 at 2:46 PM Delwakkada Liyanage, Senal Dinuka
<sdd313.msstate.edu> wrote:
>
> 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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:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Feb 20 2021 - 12:00:04 PST
