AMBER Archive (2008)

Subject: Re: AMBER: Free energy of dissociation

From: Gustavo Seabra (
Date: Thu Jun 05 2008 - 08:41:03 CDT

Hi Fatima,

If I understand correctly, you did extract the initial configuration
for all the pullings from different snapshots belonging to the same
initially equilibrated ensemble, right? That does sound right for me.
The only catch is that, in principle, this initial equilibrated
ensemble should be generated with the reaction coordinate of interest
restrained to the initial value, so that all pullings start from
(approximately) the same value of the reaction coordinate.

In this case, as long as you have a large enough number of pullings,
then taking the average of the work with the Jarzynski equation will
give you the free energy change along the path. The big question here
will be "how many pullings is enough"? To answer that, you can look at
the standard deviation. If it's not more than a few kT, you should be

Gustavo Seabra

On Thu, Jun 5, 2008 at 8:02 AM, <> wrote:
> 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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