[AMBER] PMF for dimer dissociation

From: Sanmeet Chahal <schah063.uottawa.ca>
Date: Tue, 17 Mar 2015 17:18:33 -0400

Hello All,

I need to compute a PMF for the dissociation of a dimer in TIP3P water. I
need each dimer to remain 'rigid' from an intramolecular and relative
standpoint. My PMF transformation is simply moving only one monomer away
from the other monomer with a simple translation of their atoms. The goal
of this calculation is to mimic a PB-type PMF along the separation axis but
now with proper statistics and explicit solvent.

I thought that thermodynamic integration would be the right formalism for
this in AMBER (though umbrella sampling could be more efficient).

What is the best way to compute this PMF calculation in AMBER? Any example?

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Received on Tue Mar 17 2015 - 14:30:02 PDT
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