Just a small addition to Bob's note which addresses the electrostatics correctly: Junjun is right that there will be a jump in the vdw energy. The rational normally used is that this jump at the cutoff is very small for vdw, being order r**-6 and that there are jumps in the other direction whenever an atom moves inside the cutoff so that the jumps up and down sum to zero over a simulation and even in a single step for large numbers of atoms. Finally, it has been shown by observation that using the cutoff as described with the skinnb amounts to updating the list every step and does, in fact, conserve energy.
Cheers,
Mike
On 5/12/10 10:50 AM, "Robert Duke" <rduke.email.unc.edu> wrote:
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 - 10:30:03 PDT
