4.3. Using CHARMM/APBS module
Keyword APBS inside of the PBEQ section in the CHARMM input file enters the CHARMM/APBS module. The module's keywords are as similar to the original APBS keywords as possible. However, there are several exceptions. Please read the following section carefully and also take a look at the Examples section of this User's Guide.
The following table lists all CHARMM/APBS keywords with their description. The left side of the table also lists corresponding APBS keywords which CHARMM/APBS keywords mimic very closely. For detailed discussion of APBS keywords please see APBS documentation.
4.3.1. CHARMM/APBS Module Keywords
Table 4-3. APBS and CHARMM/APBS keywords
| APBS keyword | CHARMM/APBS keyword | Description |
|---|---|---|
| APBS | Enters the APBS module | |
| mg-auto | MGAUTO | Automatically-configured sequential focusing multigrid calculation |
| mg-para | MGPARA | Automatically-configured parallel focusing multigrid calculation |
| mg-manual | MGMANUAL | Manually-configured multigrid calculation |
| lpbe/npbe | LPBE/NPBE | Linear/full Poisson-Boltzmann equation |
| 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 |
| pdie | PDIE [2.0] | Solute dielectric |
| sdie | SDIE [78.54] | 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 |
| calcenergy | CALCE [1] | Energy calculation flag: 0: Do not perform energy calculation; 1: Calculate total energy only; 2: Calculate per-atom energy components |
| calcforce | CALCF [0] | Atomic forces calculation: 0: Do not perform force calculation; 1: Calculate total force only; 2: Calculate per-atom force components |
| write pot | WPOT | Writes electrostatic potential data to iapbs-pot.dx in DX format |
| write charge | WCHG | Writes charge data to iapbs-charge.dx in DX format |
| write smol | WSMOL | Writes molecular surface data to iapbs-smol.dx in DX format |
| write kappa | WKAPPA | Writes the ion-accessibility kappa map to iapbs-kappa.dx in DX format |
| write diel | WDIEL | Writes dielectric maps to iapbs-diel[x,y,z].dx in DX format |
| read charge | RCHG | Reads charge data from iapbs-charge.dx in DX format |
| read kappa | RKAPPA | Reads the ion-accessibility kappa map from iapbs-kappa.dx in DX format |
| read diel | RDIEL | Reads dielectric maps from iapbs-diel[x,y,z].dx in DX format |
| ionq | IONQ{1|2} | Counterion charges (in e) |
| ionc | IONC{1|2} | Counterion concentrations (in M) |
| ionr | IONR{1|2} | Counterion radii (in A) |
| dime | DIMX [65] DIMY [65] DIMZ [65] | Grid dimensions (in x, y and z) |
| cmeth | CMET [1] | Centering method: 0: Center on a point 1: Center on a molecule |
| center | CNTX CNTY CNTZ | Grid center if CMET 0 |
| ccmeth | CCME [1] | Coarse grid centering method: 0: Center on a point 1: Center on a molecule |
| ccenter | CCNX CCNY CCNZ | Coarse grid center if CCME 0 |
| fcmeth | FCME [1] | Fine grid centering method: 0: Center on a point 1: Center on a molecule |
| fcenter | FCNX FCNY FCNZ | Fine grid center if FCME 0 |
| grid | GRDX GRDY GRDZ | Grid spacings |
| glen | GLNX GLNY GLNZ | Grid side lengths |
| cglen | CGLX CGLY CGLZ | Coarse grid side lengths |
| fglen | FGLX FGLY FGLZ | Fine grid side lengths |
| pdime | PDIX PDIY PDIZ | Grid of processors to be used in calculation |
| ofrac | OFRA [0.1] | Overlap fraction between processors |
| DEBUG [0] | Debuging flag | |
| UPDATE [1] | How often are solvation forces calculated during minimization or MD. Defaults to 1 which means solvation forces are updated every step. | |
| UMETHOD [1] | Method by which are solvation forces updated, when using UPDATE keyword. 0: no solvation forces are included between updates 1: forces from previous APBS calculation are used between updates | |
| SFORCE | Requests calculation of solvation forces (this keyword must be present when doing MD or minimization with APBS calculated solvation forces). |
 | Values in square brackets [] are defaults. |
4.3.2. CHARMM/APBS Notes
Each occurrence of the APBS keyword triggers APBS calculation. This not may be desirable in all cases, for example when setting up a molecular dynamics simulation with APBS calculated solvation forces. In such a case keyword SKIP in the APBS section will prevent from starting APBS calculation, the section will just initialize all APBS parameters. The actual APBS calculation will be performed when DYNAMICS section starts the simulation.
When the SFORCE keyword is specified the APBS calculation is initialized (all parameters are set) with the APBS keyword inside of the PBEQ section but the actual electrostatic calculation starts during minimization or MD step.
When performing solvation forces calculation, for example during minimization or molecular dynamics, the keywords SRFM and CHGM must be both set to 2. Also, no counterions must be present.