energy_data.dynamic_sphere — calculate soft-sphere overlap restraints

If set to True (the default), the dynamic soft-sphere overlap restraints are calculated. Note that they are only calculated if the scaled standard deviation of the soft-sphere overlap restraints is greater than zero. It is simpler not to pre-calculate any soft-sphere overlap restraints and to use the dynamically generated restraints alone, although this may be slower. The soft-sphere potential is simply a lower bound harmonic restraint (see Equation A.82), with standard deviation energy_data.sphere_stdv, dropping to zero at the sum of the two atoms' van der Waals radii.

Soft sphere restraints require the model topology to first be generated with model.generate_topology().

Automatic builds 2017-02-17