Re: [AMBER] about skinnb

From: liu junjun <ljjlp03.gmail.com>
Date: Wed, 28 Apr 2010 16:02:42 -0400

I found the code that filter off those within skinnb of nonbond list. Now I
understand. Thank you very much!

Best!

Junjun

On Wed, Apr 28, 2010 at 3:16 PM, Robert Duke <rduke.email.unc.edu> wrote:

> No, not correct. Within the energy and force evaluation routines, you LOOK
> at all entries on the nonbonded pairlist. BUT you only calculate energies,
> forces, virials (if needed) on atoms that are within cut of each other. A
> simple test without even looking at the code. Set skinnb to 2.0 and run 50
> steps. Then set skinnb to 4.0 and run 50 steps. Compare results - should
> be the same. Try same with actual change of cut by 2.0 angstrom - results
> will be slightly different.
> Regards - Bob
> (but if you look at the code, that should convince you too... ;-))
>
> ----- Original Message ----- From: "liu junjun" <ljjlp03.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Wednesday, April 28, 2010 3:05 PM
> Subject: Re: [AMBER] about skinnb
>
>
>
> Hi Bob,
>
> Thank you for your kind explanation. But I still have question. The manual
> says:
> 1. nonbonded list is extended to cut + skinnb
> 2. van der Waals and direct electrostatic interactions are truncated at cut
>
> If nonbond list is extended to cut+skinnb, then how could nonbond
> interactions be truncated at cut? As I understand by reading subroutine
> "get_nb_energy", the nonbond energies are calculated by reading whaterever
> in the nonbond list, which means the nonbond interactions are truncated
> also
> at cut+skinnb. Is this correct?
>
> Thanks!
>
> Junjun
>
> On Tue, Apr 27, 2010 at 1:32 PM, Robert Duke <rduke.email.unc.edu> wrote:
>
> The skinnb parameter is essentially an optimization parameter; by default
>> both sander and pmemd add a "skin" to the direct space cutoff length,
>> monitor the maximum atom movement every dynamics step, and only rebuild
>> the
>> pairlist when an atom has moved sufficiently far that an atom within the
>> actual cutoff distance could be missed in the calculations. If you just
>> take the default value for skinnb, everything will be fine. At least in
>> the
>> past (and maybe currently for sander - I am not sure- but never for
>> pmemd),
>> it was possible to specify rebuilding of the pairlist every nsnb (another
>> parameter) steps. This is not such a good idea, except perhaps for
>> minimizations, where I believe with sander it is the default (there is not
>> a
>> lot of actual atom movement in a minimization). You can get a more
>> complete
>> idea by looking in the manual at the descriptions of the namelist
>> variables
>> nsnb, nbflag, and skinnb.
>> Regards - Bob Duke
>> ----- Original Message ----- From: "liu junjun" <ljjlp03.gmail.com>
>> To: <amber.ambermd.org>
>> Sent: Tuesday, April 27, 2010 1:08 PM
>> Subject: [AMBER] about skinnb
>>
>>
>>
>> Hi all,
>>
>> I am trying to understand the skinnb parameter. The description for this
>> parameter in the Manual is:
>> ----------------
>> SKINNB
>> Width of the nonbonded "skin".The direct sum nonbonded list is extended to
>> cut + skinnb, and the van der Waals and direct electrostatic interactions
>> are truncated at cut. Default is 2.0 .Use of this parameter is required
>> for
>> energy conservation, and recommended for all PME runs.
>> ---------------
>>
>> My questions are:
>> 1. in subroutine "pack_nb_list" or "pack_nb_nogrdptrs" of ew_direct.f,
>> variable cutoffsq = square of (cut + skinnb)
>> variable r2 = square of distance between any nonbond pair atoms
>> The nonbond list is built by setting r2 < cutoffsq. I believe this
>> corresponds to the description that "The direct sum nonbonded list is
>> extended to cut + skinnb". However, in subroutine "get_nb_energy", I
>> notice
>> that vdw and electrostatic (eel) interactions are calculated by reading
>> whatever in the nonbond list. It looks like the vdw and eel are truncated
>> at
>> (cut+skinnb) instead of cut as stated in the Manual. Am I missing
>> something?
>>
>> 2. Can anybody please give me any references about "Use of this parameter
>> is
>> required for energy conservation"
>>
>> By the way, the source code I am reading is from AMBER8
>>
>> Thanks!
>>
>> Junjun
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Received on Wed Apr 28 2010 - 13:30:03 PDT
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