From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Thu Jan 19 2012 - 08:18:54 CST
I agree.
Boyang
On Thu, Jan 19, 2012 at 10:12 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Thu, Jan 19, 2012 at 6:55 AM, Boyang Wang <pkuwangboyang_at_gmail.com>
> wrote:
> > Hi Axel,
> >
> > if you use the interactive MD, you will see that the system volume is
>
> of course the volume changes. i didn't say that it does not.
> *but* you are confusing cause and action. the NPT integrator
> changes the volume to react to the pressure, it is not that the
> pressure fluctuates because the volume is changing like you
> are implying. the pressure *always* fluctuates, regardless of
> whether you keep the volume of your cell constant or not.
> and the pressure fluctuations are large because water (and
> most dense liquids) are not very compressible. the volume
> changes are small in comparison. since we are doing simulations
> in finite size boxes with periodic boundary conditions, we have
> a finite size effect on top of that. the pressure fluctuations are
> caused by local density fluctuations (atoms bumping into each
> other) and thus the larger your system, the smaller the fluctuations
> of the total pressure due to averaging over (uncorrelated) local
> fluctuations. it is the same with temperature (i.e. kinetic energy),
> only that the fluctuations are (relatively) much smaller.
>
> > changing. The NPT ensemble only fixes pressure, but not the volume.
>
> actually, NPT does not "fix" the pressure. it adjusts the
> volume to according to the sign and magnitude of the pressure.
>
> you get a "constant" pressure only for a system in equilibrium
> and by averaging over a longer time.
>
> axel.
>
>
> > Boyang
> >
> >
> > On Thu, Jan 19, 2012 at 7:14 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >>
> >>
> >>
> >>
> >> On Jan 19, 2012, at 3:16 AM, Boyang Wang <pkuwangboyang_at_gmail.com>
> wrote:
> >>
> >> Hi Oguz,
> >>
> >> pressure fluctuates a lot in NPT ensemble, because the volume
> fluctuates a
> >> lot. If you would like
> >>
> >>
> >> This is nonsense. The volume does *not* fluctuate a lot, it is the low
> >> compressibility of dense fluids that causes the relatively high pressure
> >> fluctuations.
> >>
> >> Axel
> >>
> >> smaller fluctuation of pressure, you can increase the Langevin piston's
> >> mass in the configuration file.
> >>
> >> Boyang
> >>
> >>
> >> On Wed, Jan 18, 2012 at 4:06 PM, oguz gurbulak <gurbulakoguz_at_yahoo.com>
> >> wrote:
> >>>
> >>> Dear All,
> >>>
> >>> I performed md simulations in NPT ensamble and got -1000 atm pressure
> >>> value for the system. My aim is to find 1 atm pressure value instead
> of a
> >>> negative pressure value. Is this problem indicates that the force
> field I
> >>> use is not appropriate for my system ? or Is this a problem caused by
> the
> >>> langevin parameters ?
> >>>
> >>> why the system did not reach the target pressure value? Could you
> please
> >>> share your thoughts about this problem ?
> >>>
> >>> Kind regards.
> >>
> >>
> >>
> >>
> >> --
> >> Boyang Wang, Ph.D.
> >>
> >
> >
> >
> > --
> > Boyang Wang, Ph.D.
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
-- Boyang Wang, Ph.D.
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:35 CST