Hi, I'm trying to simulate a complex system composed by a cluster of
AU covered by a SAM monolayer of allkylthiol chains terminating with
PEG in water. The FF that I want to use is charmm 35.
I'm trying to do equilibration of the system.
The first time I've run the simulation I hadn't any critical error and
a trajectory of 2ns, but during the simulation I obeteind about 30000
dangerous build of the neighbour list.
Then I can't complete any other simulation (starting from the same
data file) because every time (at a different timestep) I obtain an
error like :
Hi
already the dangerous builds of neighbor lists are a bad sign. This typically means either you have a unphysical state, or you choose your timestep to large (the former can be a result of the latter 
).
Anyway you could try to equilibrate with a smaller timestep first. Get as small as necessary. Also a larger neighbor bin shell can help. And you could try a minimization run first. Dangerous neighbor list builds should never ever just be ignored. They are always a sign for real trouble of which the pppm error is just another realisation.
Cheers
Christian
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