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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> > >
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> >
>
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Received on Wed Nov 11 2009 - 13:30:04 PST
