On Wed, May 12, 2010, liu junjun wrote:
>
> 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.
You are correct: the use of skinnb does not remove problems arising from
discontinuities in the Lennard-Jones terms at the cutoff. Its purpose is just
to reduce the frequency at which the non-bonded pair list needs to be
constructed.
....dac
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Received on Wed May 12 2010 - 10:00:11 PDT
