AMBER Archive (2005)

Subject: Re: AMBER: nonbond_list question .

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Sun Jun 19 2005 - 05:06:31 CDT

Hello,

I would like to note that the error described by Caoch is located two
times in AMBER8 and AMBER7 code.

AMBER8
ew_direct.f -> subroutine nonbond_list
ew_setup.f -> subroutine setup_grids

AMBER7
ew_direct.f -> subroutine ewald_list
ew_setup.f -> subroutine setup_grids

Since the reported part is executed only if periodic == 0, I assume that
the error can affect only calculation under non-periodic conditions
(vacuum and CAP simulations). If I am right this also means that the
pmemd cannot be used for the comparison because it is not able to handle
  such type of calculations.

Best regards,
        Petr

Robert Duke wrote:
> 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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>
>
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