rmsd colvar

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Sun Nov 01 2020 - 10:17:10 CST

Dear all,
I am trying to explore a conformational change in a specific domain of a
protein through metadynamics; I was wondering if it makes sense to bias
rmsd colvar for residues of the domain of interest, while harmonically
restraining the remainder residues: I am not sure to get it correctly, but
without restraints the protein would drift and rmsd calculation of the
biased domain would lose sense. Am I right?

Any considerations and hints are appreciated,
thanks in advance

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Department of Drug Science and Technology
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