On 11/2/16 5:57 AM, David De Sancho wrote: > I guess that for calculating energies of interfaces we should > care primarily for the LJ and Coulomb terms. So I have added a > make_restraints() function so that for each selection we generate > restraints for both terms.
It is almost never necessary to generate static LJ or Coulomb terms; they are generated dynamically instead - just set dyanmic_lennard=True or dynamic_coulomb=True (by default Coulomb interactions are not calculated, while soft-sphere (dynamic_sphere) interactions are used for vdw rather than LJ). Setting nonbonded_sel_atoms to 2 (as I suggested before) ensures that only interactions within each selection are counted, not interactions between the selection and the rest of the system.
Ben Webb, Modeller Caretaker