[AMBER] Accelerated MD - Please advice

From: maryam azimzadehirani <maryamai1988.gmail.com>
Date: Thu, 22 Mar 2018 15:41:41 +0100

Dear Amber Users,

I want to apply accelerate MD on a receptor-ligand system, while the ligand
is in a 20Å distant from the receptor. I want to do this to give the ligand
more freedom in sampling the phase space and not to force the final
conformation as it is done in targeted MD.

One big issue that I have is when I take the input values from the
conventional MD of the whole complex and do acceleration, I am treating
ligand residues similar as receptor residues which the may have very
different dynamical pattern. Is it fine to do this in general?

sorry if the question is preliminary...
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Received on Thu Mar 22 2018 - 08:00:02 PDT
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