On Wed, May 26, 2010 at 12:33 PM, Tom Williams <dnaafm.gmail.com> wrote:
> Thanks for the explanations from all of you!
>
> it makes some sense to me that this kind of "water holes" happens at
> the corners of a
> PBC boxe for the system of multicomponents, typically a macromolecule
> + solvent (small molecules) with large size of dimention.
>
> I have not tried the case of pure system.
> But i think this kind of "water hole" in NVT should not happen
> for whatever large size of pure system, since it is homogenous except
> that the possible case: the system condition is around at the phase
> transition region or multiphases zone (i am still doubting even at
> this condition that the hole with such nice shape
> can happen).
>
> Very welcome to everyone to follow up the list about the case of pure
> component system.
>
I would disagree here. If you don't have enough water molecules to maintain
the proper density, I can imagine this problem will surface even in a pure
water box, but again until the simulation is performed I couldn't say for
certain (I'm guessing it's already been done and published somewhere?).
All the best,
Jason
>
>
> On 5/25/10, Jason Swails <jason.swails.gmail.com> wrote:
> > Hello,
> >
> > All responses to these posts should be sent to the amber mailing list so
> > that it is archived and benefits from the attention of as many people as
> > possible...
> >
> > I'm not sure why it aggregates at the corners (though to me it would make
> > sense that the waters draw inward toward the center of the box, but since
> > it's a periodic system, I can't think of a good reason for that off the
> top
> > of my head).
> >
> > As for the pure system, any system in which the volume is not appropriate
> to
> > model the density of the system at that temperature may suffer from this
> > effect; pure or not.
> >
> > All the best,
> > Jason
> >
> > ---------- Forwarded message ----------
> > From: Tom Williams <dnaafm.gmail.com>
> > Date: Tue, May 25, 2010 at 2:50 PM
> > Subject: Re: [AMBER] Problem about Sander with large system
> > To: Bill Ross <ross.cgl.ucsf.edu>
> > Cc: jason.swails.gmail.com
> >
> >
> > Thanks for the explanations from everyone!
> >
> > My final question is if there is any particular reason that the voids
> > aggregate
> > happens *at the corners* of the *PBC box* in my case (a macromolecular
> > soaked in
> > explicit water). I am wondering if the voids aggregate also can happen in
> > a NVT
> > simulation of pure system, such as pure H2O during, the process of
> heating
> > or at
> > the constant temperature.
> >
> > Tom
> >
> >
> > On 5/26/10, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> > I am confused about your comments: "The solution is constant-pressure
> >> > equilibration."
> >> > You mean the Xleap superimpose/subtract algorithm or my MD run?
> >>
> >> Running NVT (constant volume) the smaller initial voids aggregate.
> >> Running constant pressure (NPT), the box shrinks to normal density.
> >>
> >> Bill
> >>
> >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 26 2010 - 15:30:25 PDT
