AMBER Archive (2005)

Subject: AMBER: nonbond_list question .

From: caoch_at_cherry.bio.titech.ac.jp
Date: Fri Jun 17 2005 - 20:38:27 CDT

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_at_cherry.bio.titech.ac.jp
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu