Re: [AMBER] about skinnb

From: liu junjun <ljjlp03.gmail.com>
Date: Wed, 28 Apr 2010 15:05:21 -0400

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 - 12:30:17 PDT
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