From: Stern, Julie (jvstern_at_bnl.gov)
Date: Wed May 19 2004 - 10:45:09 CDT
I'm getting a solvent banding pattern from my simulations which
I think are from a mismatch between solvent box size and the
periodic boundary condition. Is there a rule of thumb regarding
setting cellBasisVector# parameters compared to the solvent box
What started this problem was the 'atoms moving too fast' error
which seemed to go away when increasing the cellBasisVectors, but
it resulted in banding of the solvent, i.e. regions where there
is no solvent surrounded by bands of solvent. Any insight into
this? Can the 'atoms moving too fast' have come from some kind
of aliasing of the periodic boundaries?
Thanks for any help.
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