AMBER Archive (2005)

Subject: Re: AMBER: nonbond_list question .

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sat Jun 18 2005 - 22:03:07 CDT

Mike / Caoch -
I presume you all are aware that pmemd uses a completely different mechanism
(cit table driven) for doing nonbond list building? It still produces the
same results as sander, so I presume the bug below, while clearly
nonsensical, does not matter (I don't have a source machine up now, but will
have to take a look). My code is of course a bit on the complex side too,
but was engineered with speed in mind, primarily through facilitating good
cache utilization, and it does produce better performance in the various
nonbond routines.
Regards - Bob

----- Original Message -----
From: "Michael Crowley" <crowley_at_scripps.edu>
To: <caoch_at_cherry.bio.titech.ac.jp>
Cc: <amber_at_scripps.edu>
Sent: Saturday, June 18, 2005 3:51 PM
Subject: Re: AMBER: nonbond_list question .

> 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
> performance.
>
> Sincerely,
> Mike
>
> -----------------------------------------------------------------
> 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: crowley_at_scripps.edu
> Telephone: 858/784-9290
> Fax: 858/784-8688
> -----------------------------------------------------------------
>
> On Sat, 18 Jun 2005 caoch_at_cherry.bio.titech.ac.jp 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
>> --
>> caoch_at_cherry.bio.titech.ac.jp
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