Re: Periodic Box Size vs. Water Box Size

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Thu Feb 28 2008 - 11:13:45 CST

Thanks for the reply. So the box size changes in order to accomadate the
proper pressure and density? In other words, to increase pressure, the box
shrinks and to decrease pressure, the box expands. Is this correct?

Thanks,
Seth

On 2/28/08, Jeffrey J. Potoff <jpotoff_at_chem1.eng.wayne.edu> wrote:
>
> Seth Lilavivat wrote:
>
> > Dear NAMD users,
> >
> > I have a fairly basic question as a new NAMD user. Should your perodic
> > box size be as close as possible to the size of your water box? If you
> > are wrapping waters, does it not make sense then to have a periodic
> > box size that is slightly smaller than your water box to ensure there
> > is no vacuum in between water and periodic boundary?
>
>
> If you are running NPT simulations, you don't have to worry about there
> being vacuum between the water and the sides of the box. As the system
> equilibrates (molecules move around, box size changes), the vacuum will
> disappear.
>
> J.
>
> --
> ======================================================================
>
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>
>

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