[AMBER] Sufficiently equilibrated or not

From: Delwakkada Liyanage, Senal Dinuka <sdd313.msstate.edu>
Date: Sat, 20 Feb 2021 19:17:14 +0000

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.

Thank you

Senal Liyanage

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(image/png attachment: rmsd-equil100ns.png)

Received on Sat Feb 20 2021 - 11:30:03 PST
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