## File: elec.xml

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apbs 1.0.0-2
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 ELEC name id type keywords END This section is the main component for polar solvation calculations in APBS runs. There may be several ELEC sections, operating on different molecules or using different parameters for multiple runs on the same molecule. The order of the ELEC statement matters (see above); the arguments are: name id This optional command allows users to assign an alphanumeric string to the calculation to facilitate later operations (particularly in the PRINT statements). type Specify the type of electrostatics calculation to perform (these are described in greater detail below): mg-auto for automatically-configured sequential focusing multigrid calculations. mg-para for automatically-configured parallel focusing multigrid calculations. mg-manual for manually-configured multigrid calculations. fe-manual for manually-configured adaptive finite element calculations. mg-dummy for calculations of surface and charge distribution properties which do not require solution of the PBE. keywords Keywords describing the parameters of the electrostatic calculation. These are described in the Keywords section below. Automatic sequential focusing multigrid calculation (<command>mg-auto</command>) This automatically sets up and performs a string of single-point PBE calculations to "focus" on a region of interest (binding site, etc.) in a system. It is basically an automated version of mg-manual designed for easier use. Most users should probably use this version of ELEC. The keywords for this command (described in more detail in the Keywords section) are listed below. All keywords are required (no default values!) unless otherwise noted: dime cglen fglen cgcent fgcent mol lpbe or npbe or smpbe bcfl ion (optional) pdie sdie chgm usemap (optional) useaqua (optional) sdens srfm srad swin temp calcenergy calcforce write writemat Automatic parallel focusing multigrid calculation (<command>mg-para</command>) This calculation closely resembles mg-auto in syntax. However, it is basically designed to perform single-point calculations on systems in a parallel focusing fashion. While this method does provide support for decreasing the domain size from a coarse (large) global grid to a fine (smaller) global grid, it should not be used to look at subsets of biomolecules such as titration sites, etc. Such subset calculations require more complicated energy evaluation which is not yet supported by mg-para. However, since parallel focusing was designed to provide detailed evaluation of the electrostatic potential on a large scale, such subset calculations are better left to traditional focusing via the mg-auto keyword. Please note that some of the parameters change in meaning a bit for this type of calculation. In particular, dime should be interpreted as the number of grid points per processor. This interpretation helps manage the amount of memory per-processor -- generally the limiting resource for most calculations. The keywords for this command (described in more detail in the Keywords section) are listed below. All keywords are required (no default values!) unless otherwise noted: dime ofrac pdime async cglen fglen cgcent fgcent mol lpbe or npbe or smpbe bcfl ion (optional) pdie sdie chgm usemap (optional) useaqua (optional) sdens srfm srad swin temp calcenergy calcforce write writemat Manual multigrid calculation (<command>mg-manual</command>) This is the standard single-point PBE calculation performed by most solvers. The mg-manual calculation offers the most control of parameters to the user. Several of these calculations can be strung together to perform focusing calculations by judicious choice of the bcfl flag, however, the setup of the focusing is not automated as it is in mg-auto and mg-para calculations and therefore this command should only be used by more experienced users. The keywords for this command (described in more detail in the Keywords section) are listed below. All keywords are required (no default values!) unless otherwise noted: dime nlev glen or grid gcent mol lpbe or npbe or smpbe bcfl ion (optional) pdie sdie chgm usemap (optional) useaqua (optional) sdens srfm srad swin temp calcenergy calcforce write writemat Manual adaptive finite element calculation (<command>fe-manual</command>) This is a single-point PBE calculation performed by our adaptive finite element PBE solver. It requires that APBS was linked to the Holst group FEtk finite element library (http://www.fetk.org) during compilation. The finite element solver uses a "solve-estimate-refine" cycle. Specifically, starting from an initial mesh, it performs the following iteration: solve the problem estimate the error in the solution adaptively refine the mesh until a global error tolerance is reached. These methods are most useful for a select set of problems which can benefit from adaptive refinement of the solution. Furthermore, this implementation is experimental. In general, the sequential and parallel focusing multigrid methods offer the most efficient solution of the PBE for most systems The keywords for this command (described in more detail in the Keywords section) are listed below. All keywords are required (no default values!) unless otherwise noted: domainLength usemesh (optional) etol ekey akeyPRE akeySOLVE targetNum targetRes maxsolve maxvert mol lpbe or npbe or lrpbe or nrpbe bcfl ion (optional) pdie sdie chgm usemap (optional) useaqua (optional) sdens srfm srad swin temp calcenergy calcforce write writemat Manual non-numerical calculations (<command>mg-dummy</command>) This allows users to write out dielectric, ion-accessibility, and charge distribution maps based on biomolecular geometry without actually solving the PB equation. The syntax is identical to mg-dummy. The keywords for this command (described in more detail in the Keywords section) are listed below. All keywords are required (no default values!) unless otherwise noted: dime nlev cglen or grid gcent mol lpbe or npbe or smpbe bcfl ion (optional) pdie sdie chgm usemap (optional) useaqua (optional) sdens srfm srad swin temp calcenergy calcforce write writemat Keyword descriptions This is a list of keywords used in the ELEC statements of APBS. Note that not all keywords are used in every ELEC statement; see above. akeyPRE key Specify how the initial finite element mesh should be constructed (from refinement of a very coarse 8-tetrahedron mesh prior to the solve-estimate-refine iteration. This allows for various a priori refinement schemes. key The method used to guide initial refinement: unif Uniform refinement geom Geometry-based refinement at molecular surfaces and charges akeySOLVE key Specify how the the finite element mesh should be adaptively subdivided during the solve-estimate-refine iterations. This allows for various a posteriori refinement schemes. key The method used to guide adpative refinement: resi Residual-based a posteriori refinement async rank This optional keyword allows users to perform the different tasks in a parallel run asynchronously. Specifically, a processor masquerades as process rank in a parallel focusing run and provides output (data files and energies/forces) appropriate to that processor's local partition. The user must then assemble the results after all processes complete. First, this option is useful for scheduling on-demand resources: this makes it easy for users to backfill into the available processes in a queue. Second, this option is useful for running on limited resources: this enables users without access to large parallel machines to still perform the same calculations. rank The ID of the particular processor to masquerade as. Processor IDs range from 0 to N-1, where N is the total number of processors in the run (see pdime). Processor ranks are related to their position in the overall grid by p = n_x n_y k + n_x j + i where nx is the number of processors in the x-direction, ny is the number of processors in the y-direction, nz is the number of processors in the z-direction, i is the index of the processor in the x-direction, j is the index of the processor in the y-direction, k is the index of the processor in the z-direction, and p is the overall rank of the processor. bcfl flag Specify the type of boundary conditions used to solve the Poisson-Boltzmann equation: flag The flag specifying the boundary condition definition: zero "Zero" boundary condition. Potential at boundary is set to zero. This condition is not commonly used and can result in large errors if used inappropriately. sdh "Single Debye-Hückel" boundary condition. Potential at boundary is set to the values prescribed by a Debye-Hückel model for a single sphere with a point charge, dipole, and quadrupole. The sphere radius is set to the radius of the biomolecule and the sphere charge, dipole, and quadrupole are set to the total moments of the protein. This condition works best when the boundary is sufficiently far from the biomolecule. mdh "Multiple Debye-Hückel" boundary condition. Potential at boundary is set to the values prescribed by a Debye-Hückel model for a multiple, non-interacting spheres with a point charges. The sphere radii are set to the atomic radii of the biomolecule and the sphere charges are set to the total charge of the protein. This condition works better than sdh for closer boundaries but can be very slow for large biomolecules. focus "Focusing" boundary condition. Potential at boundary is set to the values computed by the previous (usually lower-resolution) PB calculation. This is used in sequential focusing performed manually in mg-manual calculations. All of the boundary points should lie within the domain of the previous calculation for best accuracy; if any boundary points lie outside, their values are computed using single Debye-Hückel boundary conditions (see above). calcenergy flag This optional keyword controls electrostatic energy output from a PBE calculation. Note that this option must be used consistently for all calculations that will appear in subsequent PRINT statements. For example, if the statement print energy 1 - 2 end appears in the input file, then both calculations 1 and 2 must have calcenergy keywords present with the same values for flag. flag Specify the types of energy values to be returned: no (Deprecated) don't calculate any energies. total Calculate and return total electrostatic energy for the entire molecule. comps Calculate and return total electrostatic energy for the entire molecule as well as electrostatic energy components for each atom. calcforce flag This optional keyword controls electrostatic and apolar force output from a PBE calculation. Note that this option must be used consistently for all calculations that will appear in subsequent PRINT statements. For example, if the statement print force 1 - 2 end appears in the input file, then both calculations 1 and 2 must have calcforce keywords present with the same values for flag. flag Specify the types of force values to be returned: no (Deprecated) don't calculate any forces. total Calculate and return total electrostatic and apolar forces for the entire molecule. comps Calculate and return total electrostatic and apolar forces for the entire molecule as well as force components for each atom. cgcent mol id xcent ycent zcent Specify the center of the coarse grid (in a focusing calculation) based on a molecule's center or absolute coordinates. The arguments for this keyword are: mol id Center the grid on molecule with ID id; as assigned in the READ section. Molecule IDs are assigned in the order they're read, starting at 1. xcent ycent zcent The coordinates (in Å) at which the grid is centered. Based on the PDB coordinate frame. cglen xlen ylen zlen Specify the coarse mesh domain lengths in a focusing calculation; this may be different in each direction. This is the starting mesh, so it should be large enough to complete enclose the biomolecule and ensure that the chosen boundary condition (see bcfl) is appropriate. xlen ylen zlen Grid lengths in the x-, y-, and z-directions in Å. chgm flag Specify the method by which the biomolecular point charges (i.e., Dirac delta functions) are mapped onto the grid. As we are attempting to model delta functions, the support (domain) of these discretized charge distributions is always a function of the grid spacing. flag Discretization method (options have multiple declarations for backward-compatibility): spl0 Traditional trilinear interpolation (linear splines). The charge is mapped onto the nearest-neighbor grid points. Resulting potentials are very sensitive to grid spacing, length, and position. spl2 Cubic B-spline discretization. The charge is mapped onto the nearest- and next-nearest-neighbor grid points. Resulting potentials are somewhat less sensitive (than spl0) to grid spacing, length, and position. spl4 Quintic B-spline discretization. Similar to spl2, except the charge/multipole is additionally mapped to include next-next-nearest neighbors (125 grid points receive charge density). dime nx ny nz Number of grid points per processor for grid-based discretization. For mg-manual, the arguments are dependent on the choice of nlev by the formula n = c 2^{l+1} + 1 where n is the dime argument, c is a non-zero integer, l is the nlev value. The most common values for grid dimensions are 65, 97, 129, and 161 (they can be different in each direction); these are all compatible with a nlev value of 4. If you happen to pick a "bad" value for the dimensions (i.e., mismatch with nlev), the code will adjust the specified dime downwards to more appropriate values. This means that "bad" values will typically result in lower resolution/accuracy calculations! The arguments for this keyword are: nx ny nz Number of grid points in the x-, y-, and z-directions. Please note that some of the parameters change in meaning a bit for this mg-para calculations. In particular, dime should be interpreted as the number of grid points per processor. This interpretation helps manage the amount of memory per-processor -- generally the limiting resource for most calculations. domainLength xlen ylen zlen Specify the rectangular finite element mesh domain lengths; this may be different in each direction. If the usemesh keyword is included, then this command is ignored. xlen ylen zlen Mesh lengths in the x-, y-, and z-directions in Å. ekey flag Specify the method used to determine the error tolerance in the solve-estimate-refine iterations of the finite element solver. flag Tolerance is interpreted as... simp ...per-simplex error limit global ...global (whole domain) error limit frac ...fraction of simplices you'd like to see refined etol tol Specify the tolerance for error-based adaptive refinement during the solve-estimate-refine iterations of the finite element solver. See also: ekey. tol The error tolerance for adaptive finite element refinement. The exact definition of this tolerance is determined by the value of ekey. fgcent mol id xcent ycent zcent Specify the center of the fine grid (in a focusing calculation) based on a molecule's center or absolute coordinates. The arguments for this keyword are: mol id Center the grid on molecule with ID id; as assigned in the READ section. Molecule IDs are assigned in the order they're read, starting at 1. xcent ycent zcent The coordinates (in Å) at which the grid is centered. Based on the PDB coordinate frame. fglen xlen ylen zlen Specify the fine mesh domain lengths in a focusing calculation; this may be different in each direction. This should enclose the region of interest in the molecule. xlen ylen zlen Grid lengths in the x-, y-, and z-directions in Å. gcent mol id xcent ycent zcent Specify the center of the grid based on a molecule's center or absolute coordinates. The arguments for this keyword are: mol id Center the grid on molecule with ID id; as assigned in the READ section. Molecule IDs are assigned in the order they're read, starting at 1. xcent ycent zcent The coordinates (in Å) at which the grid is centered. Based on the PDB coordinate frame. glen xlen ylen zlen Specify the mesh domain lengths; this may be different in each direction. For some invocations of APBS, either this key or grid must be specified. xlen ylen zlen Grid lengths in the x-, y-, and z-directions in Å. grid hx hy hz Specify the mesh grid spacings; this may be different in each direction. For some invocations of APBS, either this key or glen must be specified. hx hy hz Grid spacings in the x-, y-, and z-directions in Å. ion charge charge charge conc radius radius Specify the mobile ion species present in the system. This command can be repeated as necessary to specify multiple types of ions; however, only the largest ionic radius is used to determine the ion-accessibility function. charge Mobile ion species charge (in ec) conc Mobile ion species concentration (in M) radius Mobile ion species radius (in Å) Note that the old command syntax of ion charge conc radius is deprecated and will go away "soon". lpbe Specifies that the linearized PBE should be solved. Either this keyword or npbe nrpbe lrpbe smpbe must be present (based on the calculation type). lrpbe Specifies the linearized form of the regularized PBE equation (RPBE). The regularized PBE equation replaces the point charge distribution with the corresponding Green's function. As a result of this replacement, the solution corresponds to the reaction field instead of the total potential; the total potential can be recovered by adding the appropriate Coulombic terms to the solution. Likewise, this equation immediately yields the solvation energy without the need for reference calculations. Either this keyword or npbe nrpbe lrpbe smpbe must be present (based on the calculation type). This function is only available for FEM-based solvers. maxsolve num Specify the number of times to perform the solve-estimate-refine iteration of the finite element solver. See also: maxvert, targetRes, num Maximum number of iterations. maxvert num Specify the maximum number of vertices to allow during solve-estimate-refine cycle of finite element solver. This places a limit on the memory that can be used by the solver. See also: targetRes, maxsolve. num Maximum number of vertices. mol id Specify the molecule for which the PBE is to be solved. IDs are based on the order in which molecules are read by read mol statements, starting from 1. id The ID of the molecule for which the PBE is to be solved. nlev lev Specify the depth of the multilevel hierarchy used in the multigrid solver. See dime for a discussion of how nlev relates to grid dimensions. lev Depth of the multigrid hierarchy. npbe Specifies that the nonlinear (full) PBE should be solved. Either this keyword or npbe nrpbe lrpbe smpbe must be present (based on the calculation type). nrpbe Specifies the nonlinear form of the regularized PBE equation (RPBE). The regularized PBE equation replaces the point charge distribution with the corresponding Green's function. As a result of this replacement, the solution corresponds to the reaction field instead of the total potential; the total potential can be recovered by adding the appropriate Coulombic terms to the solution. Likewise, this equation immediately yields the solvation energy without the need for reference calculations. Either this keyword or npbe nrpbe lrpbe smpbe must be present (based on the calculation type). This function is only available for FEM-based solvers. pdie diel Specify the dielectric constant of the biomolecule. This is usually a value between 2 to 20, where lower values consider only electronic polarization and higher values consider additional polarization due to intramolecular motion. diel Biomolecular dielectric constant (unitless) pdime npx npy npz Specify the processor array to be used in a parallel focusing calculation. The product npx × npy × npz should be less than or equal to the total number of processors with which APBS was invoked (usually via mpirun). If more processors are provided at invocation than actually used during the run, the extra processors are not used in the calculation. The processors are tiled across the domain in a Cartesian fashion with a specified amount of overlap (see ofrac) between each processor to ensure continuity of the solution. Each processor's subdomain will contain the number of grid points specified by the dime keyword. npx npy npz The number of processors to be used in the x-, y- and z-directions of the system. ofrac frac Specify the amount of overlap to include between the individual processors meshes in a parallel focusing calculation (see ofrac). This should be a value between 0 and 1. frac Amount of overlap between processor meshes; a value between 0 and 1. Empirical evidence suggests that an ofrac value of 0.1 is sufficient to generate stable energies. However, this value may not be sufficient to generate stable forces and/or good quality isocontours. For example, the following table illustrates the change in energies and visual artifacts in isocontours as a function of ofrac values for a small peptide (2PHK:B). Sensitivity of 2PHK:B solvation energy calculations to <command>ofrac</command> values. ofrac value Energy (kJ/mol) Visual artifact in ± 1 kT/e iscontour? 0.05 342.79 No 0.06 342.00 No 0.07 341.12 Yes 0.08 341.14 Yes 0.09 342.02 Yes 0.10 340.84 Yes 0.11 339.67 No 0.12 341.10 No 0.13 341.10 No 0.14 341.32 No 0.15 341.54 No sdie diel Specify the dielectric constant of the solvent. Bulk water at biologically-relevant temperatures is usually modeled with a dielectric constant of 78-80. diel Solvent dielectric constant (unitless) sdens density Specify the number of grid points per square-angstrom to use in surface constructions (e.g., molecular surface, solvent-accessible surface, etc.). Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between this value used for the surface sphere density, the accuracy of the surface calculations,, and the APBS calculation time. APBS "suggested" value is 10.0. density Surface sphere density (in grid points/Å2 ). smpbe vol volume size number Specifies that the size-modified PBE should be solved as described by Chu V, et al Biophys J, in press (doi:10.1529/biophysj.106.099168). The parameter radius controls the lattice size (in Angstroms) used in the SMPBE formalism; each lattice site has a volume equal to radius3. The parameter size controls the relative size of the ions (in Angstroms) such that each lattice site can contain a single ion of volume radius3 or size ions of volume radius3/size. Either this keyword or npbe nrpbe lrpbe smpbe must be present (based on the calculation type). srad radius Specify the radius of the solvent molecules; this parameter is used to define the dielectric function (see srfm). This value is usually set to 1.4 Å for water. This keyword is ignored when any of the spline-based surfaces are used (e.g., spl2, see srfm). radius Solvent radius (in Å). swin win Specify the size of the support (i.e., the rate of change) for spline-based surface definitions (see srfm). Usually 0.3 Å. win Spline window (in Å). srfm flag Specify the model used to construct the dielectric ion-accessibility coefficients. flag The coefficient model: mol The dielectric coefficient \epsilon(x) is defined based on a molecular surface definition. The problem domain is divided into two spaces. The "free volume" space is defined by the union of solvent-sized spheres (see srad) which do not overlap with biomolecular atoms. This free volume is assigned bulk solvent dielectric values. The complement of this space is assigned biomolecular dielectric values. With a non-zero solvent radius (srad), this choice of coefficient corresponds to the traditional definition used for PB calculations. When the solvent radius is set to zero, this corresponds to a van der Waals surface definition. The ion-accessibility coefficient \overline{\kappa}^2(x) is defined by an "inflated" van der Waals model. Specifically, the radius of each biomolecular atom is increased by the radius of the ion species. The problem domain is then divided into two spaces. The space inside the union of these inflated atomic spheres is assigned an ion-accessibility value of 0; the complement space is assigned bulk ion accessibility values. smol The dielectric and ion-accessibility coefficients are defined as for mol (see above). However, they are then "smoothed" by a 9-point harmonic averaging to somewhat reduce sensitivity to the grid setup as described by Bruccoleri et al. J Comput Chem 18 268-276, 1997 (doi:10.1002/(SICI)1096-987X(19970130)18:2>268::AID-JCC11>3.0.CO;2-E). spl2 The dielectric \epsilon(x) and ion-accessibility \overline{\kappa}^2(x) coefficients are defined by a cubic-spline surface as described by Im et al, Comp Phys Commun 111 (1-3) 59-75, 1998 (doi:10.1016/S0010-4655(98)00016-2). These spline-based surface definitions are very stable with respect to grid parameters and therefore ideal for calculating forces. However, they require substantial reparameterization of the force field; interested users should consult Nina et al, Biophys Chem 78 (1-2) 89-96, 1999 (doi:10.1016/S0301-4622(98)00236-1). Additionally, these surfaces can generate unphysical results with non-zero ionic strengths; this is an on-going area of development. spl4 The dielectric and ion-accessibility coefficients are defined by a 7th order polynomial. This surface definition has characteristics similar to spl2, but provides higher order continuity necessary for stable force calculations with atomic multipole force fields (up to quadrupole). targetRes res Specify the target resolution of the simplices in the mesh; refinement will continue until the longest edge of every simplex is below this value. See also: maxvert, maxsolve, targetNum res Target resolution for longest edges of simplices in mesh (in Å). targetNum num Specify the target number of vertices in the initial mesh; intiial refinement will continue until this number is reached or the the longest edge of every simplex is below targetNum. See also: targetRes num Target number of vertices in initial mesh. temp T Temperature for PBE calculation. T Temperature (in K) useaqua This enables experimental support for Aqua, a verison of the Holst group FEtk PMG multigrid library optimized by Patrice Koehl for improved memory usage and speed when solving the Poisson-Boltzmann equation. This keyword is temporary and will eventually disappear as Aqua becomes the default multigrid solver for APBS. usemap type id Specify pre-calculated coefficient maps to be used in the PB calculation. These must have been input via an earlier read map statement. type Specify the type of pre-calculated map to be read in: diel Dielectric function map (as read by read map dielx diely dielx); this causes the pdie, sdie, srad, swin, and srfm parameters and the radii of the biomolecular atoms to be ignored when computing dielectric values for the PBE. kappa Mobile ion-accessibility function map (as read by read map kappa); this causes the swin and srfm parameters and the radii of the biomolecular atoms to be ignored when computing mobile ion values for the PBE. The ion parameter is not ignored and will still be used. charge Charge distribution map (as read by read map charge); this causes the chgm parameter and the charges of the biomolecular atoms to be ignored when assembling the fixed charge distribution for the PBE. id This ID specifies the particular map read in with read map. These IDs are assigned sequentially, starting from 1, for each map type read by APBS. usemesh id Specify the external finite element mesh to be used in the finite element PB calculation. These must have been input via an earlier read mesh statement. id This ID specifies the particular map read in with read mesh. These IDs are assigned sequentially, starting from 1, for each mesh read by APBS. write type format stem This controls the output of scalar data calculated during the PB run. This keyword can be repeated several times to provide various types of data. type What type of data to output: charge Write out the biomolecular charge distribution in units of ec (electron charge) per Angstrom3 (multigrid only). pot Write out the electrostatic potential in units of kbT/ec (multigrid and finite element) smol Write out the solvent accessibility defined by the molecular surface definition (see srfm smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) sspl Write out the spline-based solvent accessibility (see srfm spl2). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) vdw Write out the van der Waals-based solvent accessibility (see srfm smol with srad smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) ivdw Write out the inflated van der Waals-based ion accessibility (see srfm smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element) lap Write out the Laplacian of the potential \nabla^2 \phi(x) in units of kBT/ec2 (multigrid only). edens Write out the "energy density" \epsilon(x) \left( \nabla \phi \right)^2 in units of kBT/ec2 (multigrid only). ndens Write out the mobile ion number density \sum_i^m \overline{c}_i e^{-\beta q_i \phi(x)} for m ion species in units of M (multigrid only). qdens Write out the mobile charge density \sum_i^m q_i \overline{c}_i e^{-\beta q_i \phi(x)} for m ion species in units of ec M (multigrid only). dielx Write out the dielectric map shifted by 1/2 grid spacing in the x-direction (see read diel). The values are unitless (multigrid only). diely Write out the dielectric map shifted by 1/2 grid spacing in the y-direction (see read diel). The values are unitless (multigrid only). dielz Write out the dielectric map shifted by 1/2 grid spacing in the z-direction (see read diel). The values are unitless (multigrid only). kappa Write out the ion-accessibility kappa map (see read kappa). The values are in units of Å-2 (multigrid only). format Specify the format for writing out the data. dx Write out data in OpenDX format. This is the preferred format for APBS I/O. (multigrid and finite element). avs Write out data in AVS UCD format. (finite element only) uhbd Write out data in UHBD format. (multigrid only) stem Specify the path for the output; files are written to stem.XXX, where XXX is determined by the file format (and processor rank for parallel calculations). This pathname should not include spaces. writemat type stem This controls the output of the mathematical operators in the PBE as matrices in Harwell-Boeing format (multigrid only) type What type of operator to output: poission Write out the Poisson operator. pot Write out the Gateaux (functional) derivative of the full PBE operator evaluated at the current solution. stem Specify the path for the output; files are written to stem.mat. This pathname should not include spaces.