With RMSD, the issue might be more about convergence than
equilibration. But, you're certainly not ready for TI.
Which ensemble are you in? Is it NPT? If so, what does your total
energy plot vs simulation progress look like?
On Sat, Feb 20, 2021 at 2:58 PM Delwakkada Liyanage, Senal Dinuka
<sdd313.msstate.edu> wrote:
>
> 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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:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Feb 20 2021 - 14:00:02 PST
