AMBER Archive (2009)

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

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed Nov 11 2009 - 15:08:12 CST

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_at_gmail.com>
Date: Wednesday, November 11, 2009 9:54 am
Subject: Re: [AMBER] Increase Temperature to 550 K
To: AMBER Mailing List <amber_at_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_at_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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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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