Reply To: Dimer of dimers

[Anonymous]

Your symmetry definition file does not appear to allow for translational moves. Typically, the set_dof statements would look like this:

set_dof BASEJUMP x(50) angle_x(0:360) angle_y(0:360) angle_z(0:360)
set_dof JUMP2 z(50) angle_z(0:90.0)

The x(50) and z(50) items allow for translational optimization and specify that the coordinates of subunits are placed 50 A from the origin at the beginning of each simulation.

Then nstruct 9999 is probably on the low side given the number of degrees of freedom in the system.