I am running another simulation which has periodic boundary condition with three directions. I shrink the box by four steps. The >first three steps went through. But when came to the fourth, the error Bond/angle/dihedral extent > half of periodic box length >stopped the simulation. I think if it is periodic in all direction, this error does not make sense. The box is not small at all and the >volume is around 40000 ang*ang*ang when the simulation was stopped. Thank you.
Please post to the mail list, not to me.
In the current version of the code, you will get
a warning, not an error. Please download it.
The warning means what is says. You have bonds
(or angles, etc) that extend more than half the
box length. I am guessing that LAMMPS is right
and you do have those kinds of bonds (angles, etc)
and you don't realize it.