[AMBER] about skinnb

From: liu junjun <ljjlp03.gmail.com>
Date: Tue, 27 Apr 2010 13:08:48 -0400

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 - 10:30:05 PDT
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