This is what PME is all about. Stuff outside the cut is computed in the PME
algorithms in the reciprocal space calcs - with all the attendant expense of
fft's over the entire atom population. So it is not that you don't calc the
interactions past the cut - you just calculate them with a different
algorithm. You need to look over some literature/texts about the particle
mesh ewald (pme) method.
Regards - Bob Duke
----- Original Message -----
From: "liu junjun" <ljjlp03.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, May 12, 2010 12:39 PM
Subject: [AMBER] skinnb and energy conservation
> Hi all,
>
> These are the description for SKINNB in the manual:
> "The direct sum nonbonded list is extended to cut + skinnb, and the van
> der
> Waals and direct electrostatic interactions are truncated at cut."
> "Use of this parameter is required for energy conservation, and
> recommended
> for all PME runs."
>
>
> I have a question about how SKINNB works in energy conservation. The
> nonbond
> list is extended but vdw and ele interactions truncated at cut. As I
> understand, the atom pairs in the nblist can be considered as some kind of
> "candicates" for calculating vdw and ele interactions, and only those with
> distances less than cutoff are selected to calculate the vdw and ele
> interactions. If my understanding is correct, then there seems to be a
> problem in energy conservation. Lets assume there is an atom pair whose
> initial distance is 9.99A in a system where cut=10A. The nonbond
> interactions are calculated for this atom pair because 9.99A < 10A. After
> one MD step, the distance might changes to 10.01A, then the nonbond
> interactions are not calculated because 10.01 > 10A, which would cause a
> sudden energy change. If this situation happens a lot, the energy seems
> impossible to be conserved? Am I missing somethign? Can anyone please help
> me understanding this.
>
> Thanks!
>
> Junjun
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>
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Received on Wed May 12 2010 - 10:00:10 PDT
