[AMBER] Ask about the PMF generated by the ASMD simulation

From: Eleven via AMBER <amber.ambermd.org>
Date: Mon, 30 Oct 2023 16:29:33 +0800

&nbsp;Hello,&nbsp;
&nbsp; I recently used the Adaptive Steered Molecular Dynamics to do streed dynamics, and&nbsp; the PMF curve obtained after the centroid distance between the protein and the ligand has been stretched by 40Å, the PMF curve kept going up without converging. See the figure. I would like to ask if this is because I didn't stretch enough or if I had a problem with my previous processing? Looking forward to hearing from you.&nbsp; &nbsp;( The PDB of the system: 6YD4)

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Received on Mon Oct 30 2023 - 02:00:02 PDT