From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 11 2007 - 13:15:27 CDT
A uniform grid should to work fine even for PBC, though the algorithm
for PBC requires doing wraparound on the grid cells. This is the strategy
I plan to implement for adding PBC handling in some of the internal VMD
routines for things like the "within" selection and so on.
Let me know if you need help with this.
On Fri, May 11, 2007 at 04:52:49PM +0000, Arturas Ziemys wrote:
> Does anybody know some routines/algorithms to make particle distance evaluation and/or selection faster than "brute-force" way recalculating those distances directly (using PBC)? One could use some things like KDTrees, but it is useless with PBC.
> Any clues would be welcome :) !
> Arturas Z.
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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