Re: [modeller_usage] energy of interface between selections

[Modeller Caretaker <>]

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
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