Re: AMBER: nonbond_list question .

From: Michael Crowley <>
Date: Sat, 18 Jun 2005 12:51:01 -0700 (PDT)

Dear Caoch,
Your questions are gladly received, the answer to the first is a
resounding YES, you are correct, the code is in error, mea culpa.
Bugfix on the way.

As for the second, the only way to tell if the linked list is more
efficient is to try it. If my memory serves, the current method was
designed to have things as much contiguous in memory as possible.
Please feel free to try another method if you think you can improve the


Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail:
Telephone: 858/784-9290
Fax: 858/784-8688

On Sat, 18 Jun 2005 wrote:

> 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
> --
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Received on Sat Jun 18 2005 - 21:53:00 PDT
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