Re: [AMBER] Sufficiently equilibrated or not

From: Carlos Simmerling <>
Date: Sat, 20 Feb 2021 15:35:24 -0500

For ligand binding calculations, you'll want to look at the ligand pose
stability, not just overall rmsd. Is it staying where you think it should
bind? If not, then the TI calculations are unlikely to give you useful

On Sat, Feb 20, 2021, 2:17 PM Delwakkada Liyanage, Senal Dinuka <> 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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Received on Sat Feb 20 2021 - 13:00:03 PST
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