Hi Senal,
If you want to calculate the absolute binding free energy for a DNA/ligand system, I am not sure TI is the best method or not. TI is relatively computationally expensive and is not suitable for simulating alchemical processes with big configurational changes. Maybe for your case MMPBSA/MMGBSA is a better choice for calculating the absolute binding free energy?
Your RMSD became bigger and bigger, and it became relatively large after 60 ns, so it seems the trajectory was not stable and not equilibrated enough.
Hope it helps,
Pengfei
> On Feb 20, 2021, at 1:17 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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Received on Fri Feb 26 2021 - 16:00:02 PST
