From: Francesco Iori (francesco.iori_at_gmail.com)
Date: Fri Nov 17 2006 - 15:19:37 CST
Dear Namd users.
In a simulation i am trying to run i continue to have the same error
message: "bad exclusion count", which i understand is related to bad
my sistem is constituited by a number of dipoles in which one of the
two atoms is fixed and the other is not, and i am using PBC. When i
increase the charge on the two atoms of the dipole, the simulation
stops with the above error after a handful of steps. From the
trajectory is clearly seen that some atoms that should be fixed, at
some point start to move away from their original position, initially
of few tenth of angstrom (and the calculation slows down) then they
just jump off.
What i don't understand is not that the atoms jump away but why the
move at all while they should be fixed.
thanks for help
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