Hi Lin,
yes indeed the pressure is high, and pressure can have important effects.
Whether this simulation is reasonable or not depends on what you want to
learn. I think that in such cases you need to be even more careful than
usual in validating your work against experimental data. Personally I would
not trust results from such simulations unless I had some connection to
experiment. Since we don't know what data you have and want you want to
learn, it's really impossible to speculate on whether the results are
"true".
On Thu, Nov 12, 2009 at 11:36 PM, Chih-Ying Lin <chihying.usc.edu> wrote:
>
>
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 13 2009 - 06:00:06 PST
