Re: [AMBER] about skinnb

From: Robert Duke <>
Date: Wed, 28 Apr 2010 15:16:53 -0400

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" <>
To: "AMBER Mailing List" <>
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
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?



On Tue, Apr 27, 2010 at 1:32 PM, Robert Duke <> 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" <>
> To: <>
> 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:
> ----------------
> 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 - 12:30:18 PDT
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