Problem with bonds that cross periodic boundaries

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1

The pairwise atoms are turned off (via the command ‘special_bonds lj 0.0 0.0 0.0 coul 0.0 0.0 0.0’).

This doesn’t turn off pairwise interactions. This turns of pairwise 1-2, 1-3,1 -4 interactions of the bonded system
If you want to turn off pairwise interactions set the LJ coefficients to zero.

Arun

2

Thanks for clarifying, Arun. That would explain why there was no change when I increased the ghost atom cutoff distance. But, I’m still puzzled why bonds that cross periodic boundaries are problematic. -Vanessa