AMBER Archive (2008)

Subject: AMBER: Free energy of dissociation

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)