Protein simulations: why does the structure change so much?

From: Francesco Coppola (
Date: Wed Nov 10 2021 - 10:25:47 CST


I am writing to understand if it is normal that from the crystallographic
structure (pdb structure on protein data bank) to the final structure after
my simulation, that the protein changes conformation without returning to
the initial one. I tried to change damping in my parameter file, but this
doesn't seem to change the result much, as well as the timestep to 1fs
instead of 2.

There are some parameters that I particularly need to keep in mind when
simulating proteins that can affect and create errors in my simulation?

In particular the problem is related to a binding pocket that I am trying
to examine since I would like to combine them with docking analysis (where
the simulation conditions are very different).

Thank you so much for your attention and time!
Have a good day!

Best regards,
Francesco Coppola

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