Subject: Re: CCL:basic questions in MD

From: "Peter Gannett" <pgannett|at|hsc.wvu.edu>
Date: Thu, 19 Feb 2004 22:02:32 -0500

Jay:

1)  If you don't use particle Ewald mesh method, then it doesn't have
to be neutral.

2)  Read the amber manual.  There is a discussion of why the cutoff
distance is set the way it is.  

Pete

>>> Jie Zheng <jzheng73|at|u.washington.edu> 2/19/2004 6:04:32 PM >>>
Hi, CCLer:
  I have a few basic questions for molecular dynamics.
  1) why the system has to be neutral in molecular dynamics? From the
numerial point of views, it seems that to be neutral or not does not
affect the numerial algorithm. We still can get results. I know there
must
have some physical meaning behind this, anybody can give a answer?

  2) why the cutoff distance can not larger than the half-size of box?
If
we use the Ewald sum method to calculate nonbonded interactions, the
system and its images have been extend to infinite. If we use the
cutoff
method, the system is confined to the finite size by using periodic
boundary conditon. My question is that if we extend our simulation
system
to infinite as the Ewald sum does, the half-box cutoff is not required
for
the simluation systems.

   I will appreciate for your clarification.

   Jay

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From: hinsen:at:cnrs-orleans.fr
Date: Fri, 20 Feb 2004 10:04:06 +0100

> have some physical meaning behind this, anybody can give a answer?

When you use periodic boundary conditions, you are effectively  
simulating an infinite system. With a non-zero total charge, you then  
get an infinite total charge and an infinite potential energy. Such a  
system would not be stable under real-life conditions (i.e. without the  
artifact of periodic boundary conditions). In fact, if you simulate  
such a system at constant pressure, i.e. with a variable box size, you  
will see the volume go up systematically.

> to infinite as the Ewald sum does, the half-box cutoff is not required  
What you want to do in a cutoff method is to sum over all pairs of  
atoms whose distance is below the cutoff. There is indeed no physical  
reason not to have a cutoff beyond half the box size, but if you do so,  
then for consistency you have to count in some atom pairs twice,  
because both the original atom and some of its images may be within the  
cutoff distance of a given other atom. The resulting algorithm becomes  
more complicated, which is why most implementations limit themselves to  
the simple case and impose the half-box-size limit on the cutoff.
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