Dear Carlos,
So what would you answer to the work of V. Daggett ?
498 K = 225 °C
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
> what do you mean by trustworthy? there cannot possibly be an experiment of
> lysozyme NTP at 500K....
> a "good" simulation will evaporate at this T- but of course it may be
> metastable for a while first. that may vary run run to run. all of this
> really depends on what you are trying to model. as I said, there is no
> experiment to compare to, so what do you want to learn?
>
> On Wed, Nov 11, 2009 at 4:08 PM, Chih-Ying Lin <chihying.usc.edu> wrote:
>
>>
>>
>> Hi
>> The system = one lysozyme + TIP3P water
>> I was put the system in NTP simulation.
>>
>> At T <= 500 K , P =1atm
>> the simulation did not broke up.
>>
>>
>> At T = 550 K , P =1atm
>> the simulation broke up.
>>
>> under 500K, all water molecules should evaporate entirely.
>> under 550K, all water molecules should evaporate entirely.
>>
>>
>> But the simulation broke up at T=550K but not T=500K.
>> So, is it the simulation data trust-worthy at T=500K?
>>
>>
>>
>> Thank you
>> Lin
>>
>>
>> ----- Original Message -----
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Date: Wednesday, November 11, 2009 9:54 am
>> Subject: Re: [AMBER] Increase Temperature to 550 K
>> To: AMBER Mailing List <amber.ambermd.org>
>>
>> > correct- at NTP, water will boil at 550K. you need to increase P or
>> > use NVT.
>> >
>> > On Wed, Nov 11, 2009 at 10:27 AM, Chih-Ying Lin <chihying.usc.edu>
>> > wrote:
>> > >
>> > >
>> > > Hi
>> > > The system = one lysozyme + TIP3P water
>> > > I was put the system in NTP simulation.
>> > >
>> > >
>> > > Then, the simulation broke.
>> > > The following message is shown.
>> > >
>> > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b
>> > (hpc0010:0)> mpiexec: Warning: task 0 exited with status 1.
>> > > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed).
>> > > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault).
>> > >
>> > >
>> > > Anything wrong with the simulation?
>> > >
>> > > Or, under 550K, all water molecules should evaporate entirely ???
>> > >
>> > >
>> > > Thank you
>> > > Lin
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Received on Thu Nov 12 2009 - 00:00:03 PST
