Re: AMBER: About the problem of the PMEMD and cutoff

From: Robert Duke <rduke.email.unc.edu>
Date: Sun, 14 Jan 2007 23:20:22 -0500

More precisely, the cutoff radius must be less than the radius of the maximum sphere that can be contained within the unit cell (or pbc box). The reason is simple. Any atom-atom electrostatic interaction is represented by only one atom-atom pair in the code if the atom pair formed is separated by less than the cutoff radius. Under periodic boundary conditions, there are logically an infinite number of image representations for each atom, and under the typical "minimum image convention", the atom-atom pair chosen for "direct space" calculation is the image pair with minimum separation. Now, if you allow a cutoff radius greater than the maximum sphere that fits in the unit cell, it is possible that two or more images of a given atom will fall within the cutoff. These additional images would incorrectly not be accounted for in the direct space calculation. With pme, as long as the restriction on cutoff length is observed, all the other images are accounted for in reciprocal space. This really is not just a pmemd question; the condition applies to sander too.
Regards - Bob Duke
  ----- Original Message -----
  From: 方磊
  To: amber.scripps.edu
  Sent: Sunday, January 14, 2007 10:56 PM
  Subject: AMBER: About the problem of the PMEMD and cutoff


  Dear all,
     I heard from somebody that if the process of md will usi pme,the radius of the water box should be two times larger than the value of cutoff.
   
    So what does it mean? can anyone tell me?

    Thank you!


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Received on Wed Jan 17 2007 - 06:07:29 PST
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