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.
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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 26 2010 - 10:00:03 PDT
