Configuration Parameters

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).

• GBIS $<$ Use Generalized Born Implicit Solvent? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Turns on GBIS method in NAMD.

• solventDielectric $<$ dielectric of water $>$
  Acceptable Values: positive decimal
  Default Value: 78.5
  Description: Defines the dielectric of the solvent, usually 78.5 or 80.

• intrinsicRadiusOffset $<$ shrink the intrinsic radius of atoms (Å) $>$
  Acceptable Values: positive decimal
  Default Value: 0.09
  Description: This offset shrinks the intrinsic radius of atoms (used only for calculating Born radius) to give better agreement with Poisson Boltzmann calculations. Most users should not change this parameter.

• ionConcentration $<$ concentration of ions in solvent (Molar) $>$
  Acceptable Values: positive decimal
  Default Value: 0.2
  Description: An ion concentration of 0 M represents distilled water. Increasing the ion concentration increases the electrostatic screening.

• GBISDelta $<$ GB$^{OBC}$ parameter for calculating Born radii $>$
  Acceptable Values: decimal
  Default Value: 1.0
  Description: Use $\{{\tt GBISDelta}, {\tt GBISBeta},{\tt GBISGamma}\} = \{1.0, 0.8, 4.85\}$ for GB$^{OBC}$ II and $\{0.8, 0.0, 2.90912\}$ for GB$^{OBC}$ I. See $\{\alpha, \beta, \gamma\}$ in [84] for more information.

• GBISBeta $<$ GB$^{OBC}$ parameter for calculating Born radii $>$
  Acceptable Values: decimal
  Default Value: 0.8
  Description: See GBISDelta.

• GBISGamma $<$ GB$^{OBC}$ parameter for calculating Born radii $>$
  Acceptable Values: decimal
  Default Value: 4.85
  Description: See GBISDelta.

• alphaCutoff $<$ cutoff used in calculating Born radius and derivatives (phases 1 and 3) (Å) $>$
  Acceptable Values: positive decimal
  Default Value: 15
  Description: Cutoff used for calculating Born radius. Only atoms within this cutoff de-screen an atom. Though alphaCutoff can bet set to be larger or shorter than cutoff, since atom forces are more sensitive to changes in position than changes in Born radius, user's should generally set alphaCutoff to be shorter than cutoff.

• SASA $<$ whether or not to calculate SASA $>$
  Acceptable Values: on or off
  Default Value: off
  Description: The nonpolar / hydrophobic energy contribution from implicit solvent is calculated; it is proportional to the solvent-accessible surface area (SASA) which is calculated by the Linear Combination of Pairwise Overlap (LCPO) method [116]. It evaluated every nonbondedFreq steps and its energy is added into the reported ELECT energy.

• surfaceTension $<$ surface tension of SASA energy $>$
  Acceptable Values: positive decimal
  Default Value: 0.005 kcal/mol/Å$^2$
  Description: Surface tension used when calculating hydrophobic SASA energy; $E_{\rm nonpolar} = {\rm surfaceTension} \times {\rm surfaceArea}$ .

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