When using GBIS, user's should not use PME (because it is not compatible with GBIS). Periodic boundary conditions are supported but are optional. User's will need to increase cutoff; 16-18 Å is a good place to start but user's will have to check their system's behavior and increase cutoff accordingly. GBIS interactions are never excluded regardless of the type of force field used, thus user's can choose any value for exclude without affecting GBIS; user's should still choose exclude based on the force field as if using explicit solvent. When using GBIS, multiple timestepping behaves as follows: the dEdr force is calculated every nonbondedFreq steps (as with explicit solvent, 2 is a reasonable frequency) and the dEda force is calculated every fullElectFrequency steps (because dEda varies more slowly than dEdr, 4 is a reasonable frequency).
Below is a sample excerpt from a NAMD config file for nonbonded and multistep parameters when using GBIS and SASA:
#GBIS parameters GBIS on ionConcentration 0.3 alphaCutoff 14 #nonbonded parameters switching on switchdist 15 cutoff 16 pairlistdist 18 #hydrophobic energy sasa on surfaceTension 0.006 #multistep parameters timestep 1 nonbondedFreq 2 fullElectFrequency 4