4.2. Using NAMD/APBS module
The APBS module in NAMD adds implicit solvent simulation environment to the NAMD capabilities. The APBS module can be used for example for implicit solvent minimization and dynamics, calculation and visualization of miscellaneous electrostatic biomolecular properties. Please see the Examples section of this User's Guide.
The following table lists all NAMD/APBS keywords with their description. The left side of the table also lists corresponding APBS keywords which NAMD/APBS keywords mimic very closely. For detailed discussion of APBS keywords please see APBS documentation.
4.2.1. NAMD/APBS Module Keywords
Table 4-2. APBS and NAMD/APBS keywords
| APBS keyword | NAMD/APBS keyword | Description |
|---|---|---|
| apbsForces [off] | Turns on the APBS module. | |
| apbsPQRFile | PQR file name to be read. | |
| mg-auto/mg-para | calc_type [0] | 0: manual MG; 1: autoMG; 2: parallel MG |
| lpbe/nbpe | nonlin [0] | Linear/full Poisson-Boltzmann equation: 0: linear; 1: non-linear; 4: size-dependent PBE |
| bcfl | bcfl [1] | Boundary condition method: 0: zero; 1: sdh; 2: mdh; 4: focus |
| srfm | srfm [1] | Surface calculation method: 0: mol; 1: smol; 2: spl2; 3: spl4 |
| pdie | pdie [2.0] | Solute dielectric |
| sdie | sdie [78.4] | Solvent dielectric |
| sdens | sdens [10.0] | Vacc sphere density |
| srad | srad [1.4] | Solvent radius |
| swin | swin [0.3] | Cubic spline window |
| temp | temp [298.15] | Temperature (in K) |
| gamma | gamma [0.105] | Surface tension for apolar energies/forces (in kJ/mol/A^2) |
| chgm | chgm [1] | Charge discretization method: 0: spl0; 1: spl2; 2: spl4 |
| vol | smvolume [10.0] | The parameter smvolume controls the lattice size (in Angstroms^3) used in the SMPBE formalism. |
| size | smsize [1000.0] | The parameter smsize controls the relative size of the ions (in Angstroms) such that each lattice site can contain a single ion of volume radius^3 or size ions of volume radius^3/size. |
| calcenergy | calcenergy [1] | Energy calculation flag: 0: Do not perform energy calculation; 1: Calculate total energy only; 2: Calculate per-atom energy components |
| calcforce | calcforce [0] | Atomic forces calculation: 0: Do not perform force calculation; 1: Calculate total force only; 2: Calculate per-atom force components |
| calcnpenergy [1] | Calculate nonpolar energy [0, 1]. 0: Don't calculate; 1: SASA-based apolar energy caclulation. | |
| write pot | wpot [off] | Writes electrostatic potential data to iapbs-pot.dx in DX format |
| write charge | wchg [off] | Writes charge data to iapbs-charge.dx in DX format |
| write smol | wsmol [off] | Writes molecular surface data to iapbs-smol.dx in DX format |
| write kappa | wkappa [off] | Writes the ion-accessibility kappa map to iapbs-kappa.dx in DX format |
| write diel | wdiel [off] | Writes dielectric maps to iapbs-diel[x,y,z].dx in DX format |
| read charge | rchg [off] | Reads charge data from iapbs-charge.dx in DX format |
| read kappa | rkappa [off] | Reads the ion-accessibility kappa map from iapbs-kappa.dx in DX format |
| read diel | rdiel [off] | Reads dielectric maps from iapbs-diel[x,y,z].dx in DX format |
| ion | ion charge conc radius | Counterion charges (in e), Counterion concentrations (in M), Counterion radii (in A) |
| dime | dime | Grid dimensions (in x, y and z) |
| cmeth | cmeth [1] | Centering method: 0: Center on a point 1: Center on a molecule |
| gcent | center | Grid center if cmeth=0 |
| ccmeth | ccmeth [1] | Coarse grid centering method: 0: Center on a point 1: Center on a molecule |
| cgcent | ccenter | Coarse grid center if ccmeth=0 |
| fcmeth | fcmeth [1] | Fine grid centering method: 0: Center on a point 1: Center on a molecule |
| fgcent | fcenter | Fine grid center if fcmeth=0 |
| grid | grid | Grid spacings |
| glen | glen | Grid side lengths |
| cglen | cglen | Coarse grid side lengths |
| fglen | fglen | Fine grid side lengths |
| pdime | pdime | Grid of processors to be used in parallel calculation |
| ofrac | ofrac [0.1] | Overlap fraction between processors |
| debug [0] | Debugging flag [0-5] | |
| verbose [0] | Print (verbosity) flag [0-5] | |
| sp_apbs [off] | Perform a single point (a single electrostatic evaluation) APBS calculation | |
| recalculateGrid [off] | Recalculate the grid dimensions on the fly. |
 | Values in square brackets [] are defaults. |
4.2.2. NAMD/APBS Notes
When the recalculateGrid and grid keywords are set then the grid size parameters (cglen, fglen and dime) are automatically recalculated on the fly during the simulation. For example if grid is set to [0.5 0.5 0.5] Angstroms the grid size will be automatically adjusted to fit the molecule as the system's dimensions are changed during the simulation (the requested grid spacing 0.5 A will be maintained). This is the recommended option for most of simulations since this prevents the solute to "escape" the pre-set grid.
See note about disabling creation of io.mc file below before attempting any extensive minimization or MD simulation with the APBS module.