AMBER Archive (2008)

Subject: Re: AMBER: Jarzynski

From: fatima.chami_at_durham.ac.uk
Date: Sat May 31 2008 - 06:50:24 CDT

Thanks for replying.

I am working on self assembly of molecules and i am looking to the energy of
dissociation by pulling out one monomer from the aggregate. I found in the
litterature that the nonequilibrium method of Jarzynski is suitable for this.

The other way is by making one residue disappearing but for this I need to
upgrade to Amber10 which implements softcore potential

if you have any other suggestion to this I ll be happy to know

Best wishes
 
Fatima

Quoting David Mobley <dmobley_at_gmail.com>:

>
> Hi,
>
> > I want to restraint the reaction coordinate between the center of mass of
> a
> > given residue and its initial COM ... without referring to any other
> residues so
> > that
> > the constrained dynamic will be just on the residues I am interested to
> pull out
>
> For what it's worth, even if this is possible, it is probably unlikely
> to do what you want. In particular, unless you fix the rest of the
> protein in place as well, you will (at least at equilibrium) end up
> just pulling the whole protein from one place to another. That is,
> since there is nothing fixing the protein in place (no force in the
> opposite direction) pulling part of the protein away from its initial
> location will just move the whole protein away from its initial
> location.
>
> You will have to think of another way.
>
> David
>
>
> > if this is possible ..how can I set up the restraint file
> >
> > any help ...
> >
> > Best wishes
> > Fatima
> >
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