AMBER Archive (2008)

Subject: Re: AMBER: Free energy of dissociation

From: fatima.chami_at_durham.ac.uk
Date: Thu Jun 05 2008 - 10:13:03 CDT

Thanks for replying

Quoting Gustavo Seabra <gustavo.seabra_at_gmail.com>:

>
> 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.

Yes,

> 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.

I did not restraint cause the first purpose of this long simulation was to look
at the dynamics and exploit it to other calculations.
 
>
> 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.

I am pulling the same monomer and the restraint is on the relative
displacement from the initial value (let say 0.5-10 Ang)

>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
> OK.

best wishes
Fatima

>
> HTH,
> Gustavo Seabra
>
>
> On Thu, Jun 5, 2008 at 8:02 AM, <fatima.chami_at_durham.ac.uk> 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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