From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Fri Mar 25 2011 - 10:27:11 CDT
By 2D Ewald method, do you mean that you want your periodic cell
replicated infinitely along the xy-plane, but not along the z direction?
If so, then the answer is, no, NAMD does not have a specialized
method for this case, but you can accomplish this by using PME and
including enough vacuum padding so that the periodic cells no longer
"see" each other along the z direction. For a system of length L
along the z direction, it is sufficient to pad above and below by L/2
+ \delta (i.e. there must be > L vacuum between the images).
Hope this helps,
On Mar 25, 2011, at 9:49 AM, Hasan haska wrote:
> Dear NAMD users,
> Does NAMD include 2D ewald method for md simulations ?
> Thanks a lot.
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/
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