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
Received on Tue May 25 2010 - 14:00:05 PDT
