Date: Sun, 21 Feb 2021 02:33:52 +0000
Hello Dr. Foley,
Yes, the simulations were done in the NPT ensemble. I looked at the energy plots and it seemed to me that the energy convergence is attained. Below is the attached snapshot of total energy vs simulation progress plot. Also, as Dr. Simmerling suggested I looked in to the rmsd of the ligand, and the ligand was stable throughout the last 100 ns of simulation time (image attached). Nevertheless, I thought of extending my simulation time to another 100 ns due to previous fluctuations in the complex rmsd.
[cid:355520f2-ea0b-4298-8278-ed731b561041]
[cid:785d16f5-99fc-4d41-b210-bcd7636d70c1]
Thank you
Senal Liyanage
________________________________
From: Lachele Foley <lf.list.gmail.com>
Sent: Saturday, February 20, 2021 3:30 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Sufficiently equilibrated or not
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
> > > _______________________________________________
> > > AMBER mailing list
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> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
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> --
> :-) Lachele
> Lachele Foley
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