AMBER Archive (2008)

Subject: AMBER: Free energy of dissociation

From: fatima.chami_at_durham.ac.uk
Date: Thu Jun 05 2008 - 07:02:43 CDT

Dear folks,

I am looking to determine the free energy of dissociation of monomer from a
miscelle. I used the Jarzynski's approach to pull the monomer from the
miscelle along a reaction coordinate defined as the distance between their
centre of mass. The same protocol was run for several initial configuration
taken from a 150 ns MD simulation of miscelle in water.

I wondered if the average work to pull the monomer will certainly represent
the free energy of dissociation according to the Jarzynski equality.

If I have to use the Umbrella sampling approach ... I am not very clear about
the windows and the overlap ... an example of this would be great

best wishes
Fatima
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