Hello:
i want to do some modification to save CPU time. I am trying to
understand how amber building nonbond grid list. i have some questions:
1, in the nonbond_list subroutine amber write :
nogrdptrs=nogrdptrs .or.( (nucgrd1 <= 2*nghb+2) .or. &
(nucgrd1 <= 2*nghb+2) .or. &
(nucgrd1 <= 2*nghb+2) )
it seems there is a mistake in this syntax which perhaps
nogrdptrs=nogrdptrs .or.( (nucgrd1 <= 2*nghb+2) .or. &
(nucgrd2 <= 2*nghb+2) .or. &
(nucgrd3 <= 2*nghb+2) )
is it right?
2, in the grid_ucell subroutine it seems Amber does't use a linked-list
method which i thick is the most efficient way. Are there some references
of the algrithmn of building nonbond_list in AMBER?
best regards
caoch
bio center tokyo institute of technology
--
caoch.cherry.bio.titech.ac.jp
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Received on Sat Jun 18 2005 - 02:53:00 PDT
