AMBER: nonbond_list question .

From: <caoch.cherry.bio.titech.ac.jp>
Date: Sat, 18 Jun 2005 10:38:27 +0900

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
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