Binding free energy analysis at specific time interval during MD trajectory

From: Mi Yang (
Date: Thu Jul 08 2021 - 13:48:20 CDT

Dear Colleagues,
In one of our papers, we have run MD simulations for 60 ns. The RMSDs were
found reasonable stable but one reviewer asked to see what is the
difference of Binding Energy among original seeded (best docked) structure
and at some time intervals eg. at 20 ns or 30ns etc.
We have successfully extracted frames at different time intervals but
really have no idea how to calculate binding free energy for a frame
without changing specific docked structure?

We docked protein-ligand with autodock vina, prepared MD input with VMD and
ran through NAMD.
Any helpful suggestions will be highly encouraging?
Best Regards,
Dr. Shabbir

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