AMBER Archive (2009)

Subject: Re: [AMBER] Increase Temperature to 550 K

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Nov 13 2009 - 05:43:48 CST

Dear Lin,

> I set the NVT system with Temperature = 500 K.
> Then the pressure is 1780 bar.
>
> Will it be too high to be true?

I have simply reported these two papers from Daggett's group because I
thought you might be interested. Nothing more - nothing less. If we go
back to these two papers, I have the strong feeling that experience in
this field (& many tests) are required to lead to 'some' results. I do
not think that just playing with pressure will be enough, but
obviously I do not have the experience of Dr Case & Dr Simmerling in MD.

regards, Francois

>> i think it is still an open research question whether it is true
>> for most
>> proteins and unlikely that such a general statement would be true
>> for all proteins.

>> > "Increasing Temperature Accelerates Protein Unfolding
>> > Without Changing the Pathway of Unfolding"
>> >
>> > Can this statement be applied on all proteins?
>> >
>> > Thank you
>> >
>> > Lin
>> >
>> >
>> > Ferguson et al. Simulation and experiment at high temperatures:
>> > Ultrafast folding of a thermophilic protein by
>> > nucleation-condensation. Journal of Molecular Biology 2005, 347,
>> > 855-870.
>> >
>> > Day et al. Increasing Temperature Accelerates Protein Unfolding
>> > Without Changing the Pathway of Unfolding 2002, 22, 189-203.
>> >
>> > Thank you, regards, Francois
>> >
>> >
>> > ----- Original Message -----
>> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> > Date: Thursday, November 12, 2009 6:23 am
>> > Subject: Re: [AMBER] Increase Temperature to 550 K
>> > To: AMBER Mailing List <amber_at_ambermd.org>
>> >
>> > > Dave is right of course, and the only reason we need to know what
>> > > you want
>> > > to learn is to respond to your question "is this trustworthy?". I
>> > > can't try
>> > > to answer that without knowing what it is you are deciding to
>> trust.> >
>> > > On Thu, Nov 12, 2009 at 7:55 AM, case <case_at_biomaps.rutgers.edu>
>> > > wrote:
>> > > > On Thu, Nov 12, 2009, FyD wrote:
>> > > > >
>> > > > > So what would you answer to the work of V. Daggett ?
>> > > > > 498 K = 225 °C
>> > > >
>> > > > You can read Prof. Daggett's papers to find out, although the
>> > > explanation> is probably not in every paper. She is not directly
>> > > comparing her
>> > > > simulation to an experiment carried out at 498K, but rather is
>> > > using high
>> > > > temperature simulations (with special, artificial, conditions to
>> > > keep the
>> > > > density of water the same as at room temperature) to speed up
>> > > dynamical> processes. There is a long discussion and set of tests
>> > > to support the
>> > > > argument that the pathways of unfolding are not qualitatively
>> > > affected by
>> > > > such a temperature change.
>> > > >
>> > > > This (broadly speaking) would be Daggett's answer to Carlos'
>> > > question,> "what
>> > > > do you want to learn"? We don't know what your answer is; and,
>> > > of course,
>> > > > it
>> > > > may not be necessary for us to know that.
>> > > >
>> > > > ...dac

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