Hi
I set the NVT system with Temperature = 500 K.
Then the pressure is 1780 bar.
Will it be too high to be true?
Thank you
Lin
----- Original Message -----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thursday, November 12, 2009 2:30 pm
Subject: Re: [AMBER] Increase Temperature to 550 K
To: AMBER Mailing List <amber.ambermd.org>
> 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.
>
> On Thu, Nov 12, 2009 at 4:59 PM, Chih-Ying Lin <chihying.usc.edu>
> wrote:
> >
> >
> >
> > Hi
> > "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.gmail.com>
> > Date: Thursday, November 12, 2009 6:23 am
> > Subject: Re: [AMBER] Increase Temperature to 550 K
> > To: AMBER Mailing List <amber.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.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
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 12 2009 - 21:00:03 PST
