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AMBER Archive (2007)Subject: Re: AMBER: About the problem of the PMEMD and cutoff
From: Robert Duke (rduke_at_email.unc.edu)
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.
Dear all,
Thank you!
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