AMBER Archive (2008)

Subject: Re: AMBER: Jarzynski

From: David Mobley (dmobley_at_gmail.com)
Date: Mon Jun 02 2008 - 12:25:16 CDT

Hi,

> 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.

This really hasn't been done so far. In principle you could use either
PMF or nonequilibrium methods like Jarzynski's approach. Jarzynski's
approach has some known convergence difficulties that Jarzynski
himself describes (see his Phys Rev E paper from around 2002 for a
great, clear discussion). You should be sure to be aware of these and
know how you're going to get around them.

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

Wait, are these residues or "monomers" of some protein aggregate?
Residues will be a lot easier to disappear than macromolecules.

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

Just be aware that before you'll get any meaningful results on your
application of interest, there's quite a bit of new methods territory
in front of you. That is, this just hasn't been done before.

David

> 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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>
>
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