Re: [AMBER] about skinnb

From: Robert Duke <rduke.email.unc.edu>
Date: Tue, 27 Apr 2010 13:32:34 -0400

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 Tue Apr 27 2010 - 11:00:04 PDT
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