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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Received on Wed May 12 2010 - 10:00:04 PDT
