Re: Periodic Box Size vs. Water Box Size

From: Jeffrey J. Potoff (
Date: Thu Feb 28 2008 - 11:07:50 CST

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


Jeffrey J. Potoff               
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

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